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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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Liu S, Wang Q, Shao Z, Liu Q, He Y, Ren D, Yang H, Li X. Purification and Characterization of the Enzyme Fucoidanase from Cobetia amphilecti Utilizing Fucoidan from Undaria pinnatifida. Foods 2023; 12:foods12071555. [PMID: 37048377 PMCID: PMC10094035 DOI: 10.3390/foods12071555] [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: 02/02/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Fucoidanase is an unstable enzyme with high specificity that requires a large about of time to screen it from microorganisms. In this study, enzymatic hydrolysis was used to produce low-molecular-weight fucoidan from microorganisms via the degradation of high-molecular-weight fucoidan without damage to the sulfate esterification structure of oligosaccharide. The microbial strain HN-25 was isolated from sea mud and was made to undergo mutagenicity under ultraviolet light. Fucoidanase was extracted via ultrasonication and its enzymatic activity was improved via optimization of the ultrasonic conditions. The enzymatic properties and degradation efficiency of fucoidanase were characterized. The microbial strain HN-25 is a Gram-negative aerobic and rod-shaped-cell bacterium, and therefore was identified as Cobetia amphilecti via 16s rDNA. The results proved that fucoidanase is a hydrolytic enzyme with a molecular weight of 35 kDa and with high activity and stability at 30 °C and pH 8.0. The activity of fucoidanase was significantly enhanced by sodium and calcium ions and inhibited by a copper ion and ethylenediaminetetraacetate (EDTA). There was a significant decrease in the molecular weight of fucoidan after enzymatic hydrolysis. The low-molecular-weight fuicodan was divided into four fractions, mainly concentrated at F3 (20~10 kDa) and F4 (≤6 kDa). These consequences suggest that fucoidanase obtained from Cobetia amphilecti is stable and efficient and could be a good tool in the production of bioactive compounds.
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Affiliation(s)
- Shu Liu
- Colleage of Food Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
- Key Laboratory of Aquatic Products Processing and Utilization of Liaoning Province, National R and D Branch Center for Seaweed Processing, College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China
| | - Qiukuan Wang
- Key Laboratory of Aquatic Products Processing and Utilization of Liaoning Province, National R and D Branch Center for Seaweed Processing, College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China
| | - Zhenwen Shao
- Qingdao Seawit Life Science Co., Ltd., Qingdao 370200, China
| | - Qi Liu
- Bureau of Science and Technology of Qingdao West Area, Qingdao 266555, China
| | - Yunhai He
- Key Laboratory of Aquatic Products Processing and Utilization of Liaoning Province, National R and D Branch Center for Seaweed Processing, College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China
| | - Dandan Ren
- Key Laboratory of Aquatic Products Processing and Utilization of Liaoning Province, National R and D Branch Center for Seaweed Processing, College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China
| | - Hong Yang
- Colleage of Food Science and Technology, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiang Li
- Key Laboratory of Aquatic Products Processing and Utilization of Liaoning Province, National R and D Branch Center for Seaweed Processing, College of Food Science and Engineering, Dalian Ocean University, Dalian 116023, China
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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).
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Bacterial controlled mitigation of dysbiosis in a seaweed disease. THE ISME JOURNAL 2022; 16:378-387. [PMID: 34341505 PMCID: PMC8776837 DOI: 10.1038/s41396-021-01070-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023]
Abstract
Disease in the marine environment is predicted to increase with anthropogenic stressors and already affects major habitat-formers, such as corals and seaweeds. Solutions to address this issue are urgently needed. The seaweed Delisea pulchra is prone to a bleaching disease, which is caused by opportunistic pathogens and involves bacterial dysbiosis. Bacteria that can inhibit these pathogens and/or counteract dysbiosis are therefore hypothesised to reduce disease. This study aimed to identify such disease-protective bacteria and investigate their protective action. One strain, Phaeobacter sp. BS52, isolated from healthy D. pulchra, was antagonistic towards bleaching pathogens and significantly increased the proportion of healthy individuals when applied before the pathogen challenge (pathogen-only vs. BS52 + pathogen: 41-80%), and to a level similar to the control. However, no significant negative correlations between the relative abundances of pathogens and BS52 on D. pulchra were detected. Instead, inoculation of BS52 mitigated pathogen-induced changes in the epibacterial community. These observations suggest that the protective activity of BS52 was due to its ability to prevent dysbiosis, rather than direct pathogen inhibition. This study demonstrates the feasibility of manipulating bacterial communities in seaweeds to reduce disease and that mitigation of dysbiosis can have positive health outcomes.
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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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Christensen M, Jablonski P, Altermark B, Irgum K, Hansen H. High natural PHA production from acetate in Cobetia sp. MC34 and Cobetia marina DSM 4741 T and in silico analyses of the genus specific PhaC 2 polymerase variant. Microb Cell Fact 2021; 20:225. [PMID: 34930259 PMCID: PMC8686332 DOI: 10.1186/s12934-021-01713-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/28/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Several members of the bacterial Halomonadacea family are natural producers of polyhydroxyalkanoates (PHA), which are promising materials for use as biodegradable bioplastics. Type-strain species of Cobetia are designated PHA positive, and recent studies have demonstrated relatively high PHA production for a few strains within this genus. Industrially relevant PHA producers may therefore be present among uncharacterized or less explored members. In this study, we characterized PHA production in two marine Cobetia strains. We further analyzed their genomes to elucidate pha genes and metabolic pathways which may facilitate future optimization of PHA production in these strains. RESULTS Cobetia sp. MC34 and Cobetia marina DSM 4741T were mesophilic, halotolerant, and produced PHA from four pure substrates. Sodium acetate with- and without co-supplementation of sodium valerate resulted in high PHA production titers, with production of up to 2.5 g poly(3-hydroxybutyrate) (PHB)/L and 2.1 g poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)/L in Cobetia sp. MC34, while C. marina DSM 4741T produced 2.4 g PHB/L and 3.7 g PHBV/L. Cobetia marina DSM 4741T also showed production of 2.5 g PHB/L from glycerol. The genome of Cobetia sp. MC34 was sequenced and phylogenetic analyses revealed closest relationship to Cobetia amphilecti. PHA biosynthesis genes were located at separate loci similar to the arrangement in other Halomonadacea. Further genome analyses revealed some differences in acetate- and propanoate metabolism genes between the two strains. Interestingly, only a single PHA polymerase gene (phaC2) was found in Cobetia sp. MC34, in contrast to two copies (phaC1 and phaC2) in C. marina DSM 4741T. In silico analyses based on phaC genes show that the PhaC2 variant is conserved in Cobetia and contains an extended C-terminus with a high isoelectric point and putative DNA-binding domains. CONCLUSIONS Cobetia sp. MC34 and C. marina DSM 4741T are natural producers of PHB and PHBV from industrially relevant pure substrates including acetate. However, further scale up, optimization of growth conditions, or use of metabolic engineering is required to obtain industrially relevant PHA production titers. The putative role of the Cobetia PhaC2 variant in DNA-binding and the potential implications remains to be addressed by in vitro- or in vivo methods.
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Affiliation(s)
- Mikkel Christensen
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Piotr Jablonski
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Bjørn Altermark
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Knut Irgum
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Hilde Hansen
- Department of Chemistry, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
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Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods. Nat Commun 2021; 12:4160. [PMID: 34230473 PMCID: PMC8260585 DOI: 10.1038/s41467-021-24299-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 06/08/2021] [Indexed: 12/02/2022] Open
Abstract
Nitrogen fixation has a critical role in marine primary production, yet our understanding of marine nitrogen-fixers (diazotrophs) is hindered by limited observations. Here, we report a quantitative image analysis pipeline combined with mapping of molecular markers for mining >2,000,000 images and >1300 metagenomes from surface, deep chlorophyll maximum and mesopelagic seawater samples across 6 size fractions (<0.2–2000 μm). We use this approach to characterise the diversity, abundance, biovolume and distribution of symbiotic, colony-forming and particle-associated diazotrophs at a global scale. We show that imaging and PCR-free molecular data are congruent. Sequence reads indicate diazotrophs are detected from the ultrasmall bacterioplankton (<0.2 μm) to mesoplankton (180–2000 μm) communities, while images predict numerous symbiotic and colony-forming diazotrophs (>20 µm). Using imaging and molecular data, we estimate that polyploidy can substantially affect gene abundances of symbiotic versus colony-forming diazotrophs. Our results support the canonical view that larger diazotrophs (>10 μm) dominate the tropical belts, while unicellular cyanobacterial and non-cyanobacterial diazotrophs are globally distributed in surface and mesopelagic layers. We describe co-occurring diazotrophic lineages of different lifestyles and identify high-density regions of diazotrophs in the global ocean. Overall, we provide an update of marine diazotroph biogeographical diversity and present a new bioimaging-bioinformatic workflow. Nitrogen fixation by diazotrophs is critical for marine primary production. Using Tara Oceans datasets, this study combines a quantitative image analysis pipeline with metagenomic mining to provide an improved global overview of diazotroph abundance, diversity and distribution.
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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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Kazemi E, Tarhriz V, Amoozegar MA, Hejazi MS. Halomonas azerbaijanica sp. nov., a halophilic bacterium isolated from Urmia Lake after the 2015 drought. Int J Syst Evol Microbiol 2020; 71. [PMID: 33269997 DOI: 10.1099/ijsem.0.004578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, slightly halophilic bacterium, designated TBZ202T, was isolated from water of Urmia Lake, in the Azerbaijan region of north-west Iran. The strain was facultatively anaerobic, Gram-stain-negative, rod-shaped and motile. Colonies were creamy, circular, convex and shiny. It grew at NaCl concentrations of 0-12 % (w/v) (optimum 3-5 % w/v), at temperatures of 20-45 °C (optimum 30 °C) and at pH 5.0-10.0 (optimum pH 7.0). Based on the 16S rRNA gene sequence, strain TBZ202T belongs to the genus Halomonas in the Halomonadaceae and the most closely related species are Halomonas gudaonensis CGMCC 1.6133T (98.6 % similarity), Halomonas ventosae Al12T (96.8 %) and Halomonas rambilicola RS-16T (96.6%). The G+C content was 67.9 % and the digital DNA-DNA hybridization and average nucleotide identity values with H. gudaonensis were 35.8 and 83.8 %, respectively, indicating that the isolate differs from all species described. The major fatty acids were C18 : 1 ω7c, C16 : 0 and C16 : 1 ω7c. The only respiratory quinone detected was Q-9 and polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminophospholipid and three unknown phospholipids. On the basis of a polyphasic taxonomic analysis, the isolate is considered to represent a novel species of the genus Halomonas, for which the name Halomonas azerbaijanica sp. nov. is proposed. The type strain is TBZ202T (=KCTC 62817T=CECT 9693T).
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Affiliation(s)
- Elham Kazemi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Ali Amoozegar
- Extremophiles Laboratory, Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Mohammad Saeid Hejazi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
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Picon A, Del Olmo A, Nuñez M. Bacterial diversity in six species of fresh edible seaweeds submitted to high pressure processing and long-term refrigerated storage. Food Microbiol 2020; 94:103646. [PMID: 33279071 DOI: 10.1016/j.fm.2020.103646] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023]
Abstract
Seaweeds are highly perishable foods due to their richness in nutrients. High pressure processing (HPP) has been applied for extending the shelf life of fresh seaweeds but there is no information on the effect of HPP on the bacterial diversity of seaweeds. The culturable bacteria of six species of fresh edible seaweeds (green seaweeds Codium fragile and Ulva lactuca, brown seaweeds Himanthalia elongata, Laminaria ochroleuca and Undaria pinnatifida, and red seaweed Chondrus crispus) were investigated and compared to those of HPP-treated (400 and 600 MPa for 5 min) seaweeds, at the start and end of their refrigerated storage period. A total of 523 and 506 bacterial isolates were respectively retrieved from untreated and HPP-treated seaweeds. Isolates from untreated seaweeds belonged to 18 orders, 35 families, 71 genera and 135 species whereas isolates from HPP-treated seaweeds belonged to 13 orders, 23 families, 43 genera and 103 species. HPP treatment significantly reduced the number of isolates belonging to 6 families and greatly increased the number of Bacillaceae isolates. At the end of storage, decreases in bacterial diversity at the genus and species level were observed for untreated as well as for HPP-treated seaweeds.
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Affiliation(s)
- Antonia Picon
- INIA, Departamento de Tecnología de Alimentos, Carretera de La Coruña Km 7, 28040, Madrid, Spain.
| | - Ana Del Olmo
- INIA, Departamento de Tecnología de Alimentos, Carretera de La Coruña Km 7, 28040, Madrid, Spain
| | - Manuel Nuñez
- INIA, Departamento de Tecnología de Alimentos, Carretera de La Coruña Km 7, 28040, Madrid, Spain
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Moriya H, Takita Y, Matsumoto A, Yamahata Y, Nishimukai M, Miyazaki M, Shimoi H, Kawai SJ, Yamada M. Cobetia sp. Bacteria, Which Are Capable of Utilizing Alginate or Waste Laminaria sp. for Poly(3-Hydroxybutyrate) Synthesis, Isolated From a Marine Environment. Front Bioeng Biotechnol 2020; 8:974. [PMID: 32984275 PMCID: PMC7479843 DOI: 10.3389/fbioe.2020.00974] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/27/2020] [Indexed: 11/13/2022] Open
Abstract
We isolated the Cobetia sp. strains IU 180733JP01 (5-11-6-3) and 190790JP01 (5-25-4-2) from seaweeds and showed that both strains accumulate poly(3-hydroxybutyrate) [P(3HB)] homopolymer in a nitrogen-limiting mineral salt medium containing alginate as a sole carbon source. Genome sequence analysis of the isolated strains showed that they have putative genes which encode enzymes relevant to alginate assimilation and P(3HB) synthesis, and the putative alginate-assimilating genes formed a cluster. Investigation of the optimum culture conditions for high accumulation of P(3HB) showed that when the 5-11-6-3 strain was cultured in a nitrogen-limiting mineral salt medium (pH 5.0) containing 6% NaCl and 3% (w/v) alginate as a sole carbon source for 2 days, the P(3HB) content and P(3HB) production reached 62.1 ± 3.4 wt% and 3.11 ± 0.16 g/L, respectively. When the 5-25-4-2 strain was cultured in a nitrogen-limiting mineral salt medium (pH 4.0) containing 5% NaCl and 3% (w/v) alginate for 2 days, the P(3HB) content and P(3HB) production reached 56.9 ± 2.1 wt% and 2.67 ± 0.11 g/L, respectively. Moreover, the 5-11-6-3 strain also produced P(3HB) in a nitrogen-limiting mineral salt medium (pH 5.0) containing 6% NaCl and freeze-dried and crushed waste Laminaria sp., which is classified into brown algae and contains alginate abundantly. The resulting P(3HB) content and P(3HB) productivity were 13.5 ± 0.13 wt% and 3.99 ± 0.15 mg/L/h, respectively. Thus, we demonstrated the potential application of the isolated strains to a simple P(3HB) production process from seaweeds without chemical hydrolysis and enzymatic saccharification.
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Affiliation(s)
- Hiroki Moriya
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Yuto Takita
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Akira Matsumoto
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Yuki Yamahata
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Megumi Nishimukai
- Department of Animal Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Masao Miyazaki
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Hitoshi Shimoi
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
| | - Sung-Jin Kawai
- New Field Pioneering Division, New Value Creation Center, Toyota Boshoku Corporation, Kariya, Japan
| | - Miwa Yamada
- Department of Biological Chemistry and Food Science, Iwate University, Morioka, Japan
- Education and Research on Sanriku Fishery Industry Department, Organization for Revitalization of the Sanriku Region and Regional Development, Iwate University, Morioka, Japan
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12
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Gnaim R, Golberg A, Sheviryov J, Rubinsky B, González CA. Detection and differentiation of bacteria by electrical bioimpedance spectroscopy. Biotechniques 2020; 69:384-394. [PMID: 32486835 DOI: 10.2144/btn-2019-0080] [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] [Indexed: 11/23/2022] Open
Abstract
Detecting bacteria in samples and differentiating between Gram-negative and Gram-positive species is an important challenge, and the most common method, Gram staining, is very time consuming. The aim of this study was to evaluate the electrical bioimpedance spectroscopy (EBIS) technique as an inexpensive and practical tool for real-time detection of bacteria and differentiation between Gram-positive and Gram-negative species. The relevant sensitivity for differentiating between species was found in the magnitude and phase at frequencies of 158,489 and 5248 Hz, respectively, at a bacterial concentration of 1 μg/μl. Subsequently, the sensitivity was estimated as a function of bacterial concentration. Our results demonstrated that EBIS can potentially distinguish between presence and absence of bacteria as well as between different types of bacteria.
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Affiliation(s)
- Rima Gnaim
- Porter School of Environment & Earth Sciences, Tel Aviv University. Tel Aviv-Yafo, Israel.,The Triangle Regional Research & Development Center, Kfar Qari' 30075, Israel
| | - Alexander Golberg
- Porter School of Environment & Earth Sciences, Tel Aviv University. Tel Aviv-Yafo, Israel
| | - Julia Sheviryov
- Porter School of Environment & Earth Sciences, Tel Aviv University. Tel Aviv-Yafo, Israel
| | - Boris Rubinsky
- Mechanical Engineering Department, University of California-Berkeley, CA, USA
| | - César A González
- Porter School of Environment & Earth Sciences, Tel Aviv University. Tel Aviv-Yafo, Israel.,Escuela Superior de Medicina-Instituto Politécnico Nacional, Mexico City, Mexico
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13
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Lelchat F, Mocaer PY, Ojima T, Michel G, Sarthou G, Bucciarelli E, Cérantola S, Colliec-Jouault S, Boisset C, Baudoux AC. Viral degradation of marine bacterial exopolysaccharides. FEMS Microbiol Ecol 2020; 95:5498295. [PMID: 31125051 DOI: 10.1093/femsec/fiz079] [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] [Received: 01/25/2019] [Accepted: 05/23/2019] [Indexed: 11/14/2022] Open
Abstract
The identification of the mechanisms by which marine dissolved organic matter (DOM) is produced and regenerated is critical to develop robust prediction of ocean carbon cycling. Polysaccharides represent one of the main constituents of marine DOM and their degradation is mainly attributed to polysaccharidases derived from bacteria. Here, we report that marine viruses can depolymerize the exopolysaccharides (EPS) excreted by their hosts using five bacteriophages that infect the notable EPS producer, Cobetia marina DSMZ 4741. Degradation monitorings as assessed by gel electrophoresis and size exclusion chromatography showed that four out of five phages carry structural enzymes that depolymerize purified solution of Cobetia marina EPS. The depolymerization patterns suggest that these putative polysaccharidases are constitutive, endo-acting and functionally diverse. Viral adsorption kinetics indicate that the presence of these enzymes provides a significant advantage for phages to adsorb onto their hosts upon intense EPS production conditions. The experimental demonstration that marine phages can display polysaccharidases active on bacterial EPS lead us to question whether viruses could also contribute to the degradation of marine DOM and modify its bioavailability. Considering the prominence of phages in the ocean, such studies may unveil an important microbial process that affects the marine carbon cycle.
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Affiliation(s)
- F Lelchat
- Laboratoire BMM, centre Ifremer de Brest, ZI pointe du diable, 29280 Plouzané, France
| | - P Y Mocaer
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - T Ojima
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Minato-cho 3-1-1, Hakodate 041-8611, Japan
| | - G Michel
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Modèles Marins UMR 8227, Station Biologique de Roscoff, Roscoff, France
| | - G Sarthou
- CNRS, Université de Brest, IRD, Ifremer, UMR 6539/LEMAR/IUEM, Technopôle Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France
| | - E Bucciarelli
- CNRS, Université de Brest, IRD, Ifremer, UMR 6539/LEMAR/IUEM, Technopôle Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France
| | - S Cérantola
- Service commun de résonnance magnétique nucléaire, Faculté de science de Brest, Université de Bretagne Occidentale, 6 av. Victor Le Gorgeu, 29238 Brest Cedex 3, France
| | - S Colliec-Jouault
- Laboratoire EM3B, Centre Ifremer Atlantique - Rue de l'Ile d'Yeu - 44311 Nantes, France
| | - C Boisset
- Service commun de chromatographie, CERMAV-CNRS, 601 rue de la chimie, St Martin d'Hère, 38041 Grenoble, France
| | - A-C Baudoux
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
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14
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Mei R, Zhou M, Xu L, Zhang Y, Su X. Characterization of a pH-Tolerant Strain Cobetia sp. SASS1 and Its Phenol Degradation Performance Under Salinity Condition. Front Microbiol 2019; 10:2034. [PMID: 31551971 PMCID: PMC6737460 DOI: 10.3389/fmicb.2019.02034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/19/2019] [Indexed: 11/13/2022] Open
Abstract
Biological treatment of complex saline phenolic wastewater remains a great challenge due to the low activity of bacterial populations under stressful conditions. Acid mine drainage (AMD) as a typically extreme environment, shaped unique AMD microbial communities. Microorganisms survived in the AMD environment have evolved various mechanisms of resistance to low pH, high salinity and toxic heavy metals. The primary goal of this work was to determine whether a strain isolated from an AMD could degrade phenol under stressful conditions such as low pH, high salinity and heavy metals. The results suggested that the strain Cobetia sp. SASS1 isolated from AMD presented different physiological characteristics in comparison with five most closely related species. SASS1 can efficiently degrade phenol at wide ranges of pH (3.0-9.0) and NaCl concentration (0-40 g/L), as well as the existence of Cu2+ and Mn2+. Specifically, the SASS1 could completely degrade 1500 mg/L phenol in 80 h at 10 g/L NaCl. Meanwhile, mineralization of phenol was achieved with complete degradation of 900 mg/L phenol and simultaneously COD decreasing from 2239 mg/L to 181.6 mg/L in 36 h. Based on biodegradation metabolites identification and enzyme activities analysis, both ortho-cleavage pathway and benzoic acid pathway for phenol degradation were proposed. These findings suggested that SASS1 was an efficient phenol degrader under salinity and acidic conditions, and could be considered as key population for bioremediation of industrial phenolic wastewaters under stressful conditions.
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Affiliation(s)
- Rongwu Mei
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou, China
| | - Meng Zhou
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, China
| | - Luning Xu
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, China
| | - Yu Zhang
- Environmental Science Research and Design Institute of Zhejiang Province, Hangzhou, China
| | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, China
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15
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Ullah R, Yasir M, Bibi F, Abujamel TS, Hashem AM, Sohrab SS, Al-Ansari A, Al-Sofyani AA, Al-Ghamdi AK, Al-Sieni A, Azhar EI. Taxonomic diversity of antimicrobial-resistant bacteria and genes in the Red Sea coast. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 677:474-483. [PMID: 31063890 DOI: 10.1016/j.scitotenv.2019.04.283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/26/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Despite development of a record number of recreational sites and industrial zones on the Red Sea coast in the last decade, antibiotic-resistant bacteria in this environment remain largely unexplored. In this study, 16S rDNA sequencing was used to identify bacteria isolated from 12 sediment samples collected from the Red Sea coastal, offshore, and mangroves sites. Quantitative PCR was used to estimate the quantity of antimicrobial resistance genes (ARGs) in genomic DNA in the samples. A total of 470 bacteria were isolated and classified into 137 distinct species, including 10 candidate novel species. Site-specific bacterial communities inhabiting the Red Sea were apparent. Relatively, more resistant isolates were recovered from the coast, and samples from offshore locations contained the most multidrug-resistant bacteria. Eighteen ARGs were detected in this study encoding resistance to aminoglycoside, beta-lactam, sulfonamide, macrolide, quinolone, and tetracycline antibiotics. The qnrS, aacC2, ermC, and blaTEM-1 genes were commonly found in coastal and offshore sites. Relatively higher abundance of ARGs, including aacC2 and aacC3, were found in the apparently anthropogenically contaminated (beach) samples from coast compared to other collected samples. In conclusion, a relative increase in antimicrobial-resistant isolates was found in sediment samples from the Red Sea, compared to other studies. Anthropogenic activities likely contribute to this increase in bacterial diversity and ARGs.
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Affiliation(s)
- Riaz Ullah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Turki S Abujamel
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Al-Ansari
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulmohsin A Al-Sofyani
- Marine Biology Department, Faculty of Marine Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed K Al-Ghamdi
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulbasit Al-Sieni
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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16
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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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17
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Martínez-Gutiérrez CA, Latisnere-Barragán H, García-Maldonado JQ, López-Cortés A. Screening of polyhydroxyalkanoate-producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico. PeerJ 2018; 6:e4780. [PMID: 29761063 PMCID: PMC5944434 DOI: 10.7717/peerj.4780] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/23/2018] [Indexed: 11/20/2022] Open
Abstract
Hypersaline microbial mats develop through seasonal and diel fluctuations, as well as under several physicochemical variables. Hence, resident microorganisms commonly employ strategies such as the synthesis of polyhydroxyalkanoates (PHAs) in order to resist changing and stressful conditions. However, the knowledge of bacterial PHA production in hypersaline microbial mats has been limited to date, particularly in regard to medium-chain length PHAs (mcl-PHAs), which have biotechnological applications due to their plastic properties. The aim of this study was to obtain evidence for PHA production in two hypersaline microbial mats of Guerrero Negro, Mexico by searching for PHA granules and PHA synthase genes in isolated bacterial strains and environmental samples. Six PHA-producing strains were identified by 16S rRNA gene sequencing; three of them corresponded to a Halomonas sp. In addition, Paracoccus sp., Planomicrobium sp. and Staphylococcus sp. were also identified as PHA producers. Presumptive PHA granules and PHA synthases genes were detected in both sampling sites. Moreover, phylogenetic analysis showed that most of the phylotypes were distantly related to putative PhaC synthases class I sequences belonging to members of the classes Alphaproteobacteria and Gammaproteobacteria distributed within eight families, with higher abundances corresponding mainly to Rhodobacteraceae and Rhodospirillaceae. This analysis also showed that PhaC synthases class II sequences were closely related to those of Pseudomonas putida, suggesting the presence of this group, which is probably involved in the production of mcl-PHA in the mats. According to our state of knowledge, this study reports for the first time the occurrence of phaC and phaC1 sequences in hypersaline microbial mats, suggesting that these ecosystems may be a novel source for the isolation of short- and medium-chain length PHA producers.
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Affiliation(s)
- Carolina A Martínez-Gutiérrez
- Laboratorio de Geomicrobiología y Biotecnología, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
| | - Hever Latisnere-Barragán
- Laboratorio de Geomicrobiología y Biotecnología, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Alejandro López-Cortés
- Laboratorio de Geomicrobiología y Biotecnología, Centro de Investigaciones Biológicas del Noroeste, La Paz, Baja California Sur, México
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18
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Guo H, Rischer M, Sperfeld M, Weigel C, Menzel KD, Clardy J, Beemelmanns C. Natural products and morphogenic activity of γ-Proteobacteria associated with the marine hydroid polyp Hydractinia echinata. Bioorg Med Chem 2017; 25:6088-6097. [PMID: 28893599 PMCID: PMC5675742 DOI: 10.1016/j.bmc.2017.06.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/21/2017] [Accepted: 06/30/2017] [Indexed: 02/07/2023]
Abstract
Illumina 16S rRNA gene sequencing was used to profile the associated bacterial community of the marine hydroid Hydractinia echinata, a long-standing model system in developmental biology. 56 associated bacteria were isolated and evaluated for their antimicrobial activity. Three strains were selected for further in-depth chemical analysis leading to the identification of 17 natural products. Several γ-Proteobacteria were found to induce settlement of the motile larvae, but only six isolates induced the metamorphosis to the primary polyp stage within 24h. Our study paves the way to better understand how bacterial partners contribute to protection, homeostasis and propagation of the hydroid polyp.
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Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Maja Rischer
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Martin Sperfeld
- Department of Applied and Ecological Microbiology, Institute for Microbiology, Friedrich Schiller University Jena, Philosophenweg 12, D-07743 Jena, Germany
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Klaus Dieter Menzel
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany
| | - Jon Clardy
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Harvard University, 240 Longwood Ave., Boston, MA 02115, USA
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Beutenbergstraβe 11a, D-07745 Jena, Germany.
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Genome Sequence of Cobetia sp. Strain MM1IDA2H-1, a Hydrocarbon-Degrading and Biosurfactant-Producing Marine Bacterium. GENOME ANNOUNCEMENTS 2017; 5:5/15/e00132-17. [PMID: 28408668 PMCID: PMC5391406 DOI: 10.1128/genomea.00132-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cobetia sp. strain MM1IDA2H-1 is a marine bacterium isolated from seawater samples that uses the heterocyclic aromatic hydrocarbon dibenzothiophene as the sole carbon source and produces a biosurfactant that inhibits bacterial quorum sensing. The Cobetia sp. MM1IDA2H-1 genome was sequenced, processed, assembled, and annotated for basic and applied studies.
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20
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Kokoulin MS, Kuzmich AS, Kalinovsky AI, Tomshich SV, Romanenko LA, Mikhailov VV, Komandrova NA. Structure and anticancer activity of sulfated O-polysaccharide from marine bacterium Cobetia litoralis KMM 3880 T. Carbohydr Polym 2016; 154:55-61. [DOI: 10.1016/j.carbpol.2016.08.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/11/2016] [Accepted: 08/11/2016] [Indexed: 11/16/2022]
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21
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Balabanova L, Nedashkovskaya O, Podvolotskaya A, Slepchenko L, Golotin V, Belik A, Shevchenko L, Son O, Rasskazov V. Data supporting functional diversity of the marine bacterium Cobetia amphilecti KMM 296. Data Brief 2016; 8:726-32. [PMID: 27508225 PMCID: PMC4949733 DOI: 10.1016/j.dib.2016.06.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 05/21/2016] [Accepted: 06/21/2016] [Indexed: 11/17/2022] Open
Abstract
Data is presented in support of functionality of hyper-diverse protein families encoded by the Cobetia amphilecti KMM 296 (formerly Cobetia marina KMM 296) genome (“The genome of the marine bacterium Cobetia marina KMM 296 isolated from the mussel Crenomytilus grayanus (Dunker, 1853)” [1]) providing its nutritional versatility, adaptability and biocontrol that could be the basis of the marine bacterium evolutionary and application potential. Presented data include the information of growth and biofilm-forming properties of the food-associated isolates of Pseudomonas, Bacillus, Listeria, Salmonella and Staphylococcus under the conditions of their co-culturing with C. amphilecti KMM 296 to confirm its high inter-species communication and anti-microbial activity. Also included are the experiments on the crude petroleum consumption by C. amphilecti KMM 296 as the sole source of carbon in the presence of sulfate or nitrate to ensure its bioremediation capacity. The multifunctional C. amphilecti KMM 296 genome is a promising source for the beneficial psychrophilic enzymes and essential secondary metabolites.
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Affiliation(s)
- Larissa Balabanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation; School of Economics and Management, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Olga Nedashkovskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation
| | - Anna Podvolotskaya
- School of Economics and Management, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Lubov Slepchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation; School of Economics and Management, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Vasily Golotin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation; School of Economics and Management, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Alexey Belik
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation
| | - Ludmila Shevchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation
| | - Oksana Son
- School of Economics and Management, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Valery Rasskazov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russian Federation
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Zepeda VK, Busse HJ, Golke J, Saw JHW, Alam M, Donachie SP. Terasakiispira papahanaumokuakeensis gen. nov., sp. nov., a gammaproteobacterium from Pearl and Hermes Atoll, Northwestern Hawaiian Islands. Int J Syst Evol Microbiol 2015; 65:3609-3617. [PMID: 26297573 DOI: 10.1099/ijsem.0.000438] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, helical bacterium designated PH27AT was cultivated from an anchialine pool on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The obligately halophilic strain was motile by bipolar tufts of flagella and grew optimally at pH 7, and microaerobically or aerobically. Closest neighbours based on 16S rRNA gene nucleotide sequence identity are Marinospirillum celere v1c_Sn-redT (93.31 %) and M. alkaliphilum Z4T (92.10 %) in the family Oceanospirillaceae, class Gammaproteobacteria. PH27AT is distinguished phenotypically from members of the genus Marinospirillum by its hydrolysis of gelatin, the absence of growth in media containing ≤ 1 % (w/v) NaCl and the ranges of temperature (12–40 °C) and pH (5–8) for growth. The major compound ubiquinone Q-9 distinguishes the quinone system of strain PH27AT from those in members of the genus Marinospirillum and other members of the Oceanospirillaceae, in which the major quinone is Q-8. Major polar lipids in PH27AT were phosphatidylethanolamine and phosphatidylglycerol, with moderate amounts of diphosphatidylglycerol and phosphatidylserine. Spermidine and cadaverine dominated the polyamine pattern; large proportions of cadaverine have not been reported in members of the genus Marinospirillum. Genotypic and chemotaxonomic data show that PH27AT does not belong in the genus Marinospirillum or other genera of the family Oceanospirillaceae or the Halomonadaceae. We propose a new genus, Terasakiispira gen. nov., be created to accommodate Terasakiispira papahanaumokuakeensis gen. nov., sp. nov. as the type species, with PH27AT ( = ATCC BAA-995T = DSM 16455T = DSM 23961T) as the type strain.
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Affiliation(s)
- Vanessa K Zepeda
- Department of Microbiology, University of Hawai'i at Ma¯noa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Jan Golke
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Jimmy H W Saw
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Maqsudul Alam
- Department of Microbiology, University of Hawai'i at Ma¯noa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
| | - Stuart P Donachie
- Department of Microbiology, University of Hawai'i at Ma¯noa, Snyder Hall, 2538 McCarthy Mall, Honolulu, HI 96822, USA
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Kokoulin MS, Kalinovsky AI, Komandrova NA, Tomshich SV, Romanenko LA, Vaskovsky VE. The new sulfated O-specific polysaccharide from marine bacterium Cobetia pacifica KMM 3878, containing 3,4-O-[(S)-1-carboxyethylidene]-d-galactose and 2,3-O-disulfate-d-galactose. Carbohydr Res 2014; 397:46-51. [DOI: 10.1016/j.carres.2014.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/27/2014] [Accepted: 06/06/2014] [Indexed: 10/25/2022]
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Kim KK, Lee JS, Stevens DA. Microbiology and epidemiology of Halomonas species. Future Microbiol 2014; 8:1559-73. [PMID: 24266356 DOI: 10.2217/fmb.13.108] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Halomonas has been organized as a genus since 1980, and comprises halophilic and/or halotolerant Gram-negative aerobic bacteria, typically found in saline environments. The genus is enlarging: at present, 76 species are taxonomically recognized, with more to be added. Increasing industrial uses have been found, largely in bioremediation and the production of desirable compounds. Originally seen as environmental contaminants, pathogenicity was initially not recognized; however, disease in algae, animals and humans has now been described. As the biotechnological use of these species increases, and the ability to isolate and recognize them improves, one might expect further pathogenic encounters with humans to be described.
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Affiliation(s)
- Kwang Kyu Kim
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience & Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Cluff MA, Hartsock A, MacRae JD, Carter K, Mouser PJ. Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:6508-17. [PMID: 24803059 DOI: 10.1021/es501173p] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process.
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Affiliation(s)
- Maryam A Cluff
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University , Columbus, Ohio 43210, United States
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Kokoulin MS, Kalinovsky AI, Komandrova NA, Tomshich SV, Romanenko LA, Vaskovsky VE. The sulfated O-specific polysaccharide from the marine bacterium Cobetia pacifica KMM 3879T. Carbohydr Res 2014; 387:4-9. [DOI: 10.1016/j.carres.2014.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/13/2014] [Accepted: 01/15/2014] [Indexed: 10/25/2022]
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Ibacache-Quiroga C, Ojeda J, Espinoza-Vergara G, Olivero P, Cuellar M, Dinamarca MA. The hydrocarbon-degrading marine bacterium Cobetia sp. strain MM1IDA2H-1 produces a biosurfactant that interferes with quorum sensing of fish pathogens by signal hijacking. Microb Biotechnol 2013; 6:394-405. [PMID: 23279885 PMCID: PMC3917474 DOI: 10.1111/1751-7915.12016] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 11/12/2012] [Accepted: 11/14/2012] [Indexed: 11/27/2022] Open
Abstract
Biosurfactants are produced by hydrocarbon-degrading marine bacteria in response to the presence of water-insoluble hydrocarbons. This is believed to facilitate the uptake of hydrocarbons by bacteria. However, these diffusible amphiphilic surface-active molecules are involved in several other biological functions such as microbial competition and intra-or inter-species communication. We report the isolation and characterization of a marine bacterial strain identified as Cobetia sp. MM1IDA2H-1, which can grow using the sulfur-containing heterocyclic aromatic hydrocarbon dibenzothiophene (DBT). As with DBT, when the isolated strain is grown in the presence of a microbial competitor, it produces a biosurfactant. Because the obtained biosurfactant was formed by hydroxy fatty acids and extracellular lipidic structures were observed during bacterial growth, we investigated whether the biosurfactant at its critical micelle concentration can interfere with bacterial communication systems such as quorum sensing. We focused on Aeromonas salmonicida subsp. salmonicida, a fish pathogen whose virulence relies on quorum sensing signals. Using biosensors for quorum sensing based on Chromobacterium violaceum and Vibrio anguillarum, we showed that when the purified biosurfactant was mixed with N-acyl homoserine lactones produced by A. salmonicida, quorum sensing was inhibited, although bacterial growth was not affected. In addition, the transcriptional activities of A. salmonicida virulence genes that are controlled by quorum sensing were repressed by both the purified biosurfactant and the growth in the presence of Cobetia sp. MM1IDA2H-1. We propose that the biosurfactant, or the lipid structures interact with the N-acyl homoserine lactones, inhibiting their function. This could be used as a strategy to interfere with the quorum sensing systems of bacterial fish pathogens, which represents an attractive alternative to classical antimicrobial therapies in fish aquaculture.
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Affiliation(s)
- C Ibacache-Quiroga
- Laboratorio de Biotecnología Microbiana, Universidad de Valparaíso, Valparaíso, Chile
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