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Li X, Cui Y, Wu W, Zhang Z, Fang J, Yu X, Cao J. Characterization and Biosynthetic Regulation of Isoflavone Genistein in Deep-Sea Actinomycetes Microbacterium sp. B1075. Mar Drugs 2024; 22:276. [PMID: 38921587 PMCID: PMC11205022 DOI: 10.3390/md22060276] [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: 05/08/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/27/2024] Open
Abstract
Deep-sea environments, as relatively unexplored extremes within the Earth's biosphere, exhibit notable distinctions from terrestrial habitats. To thrive in these extreme conditions, deep-sea actinomycetes have evolved unique biochemical metabolisms and physiological capabilities to ensure their survival in this niche. In this study, five actinomycetes strains were isolated and identified from the Mariana Trench via the culture-dependent method and 16S rRNA sequencing approach. The antimicrobial activity of Microbacterium sp. B1075 was found to be the most potent, and therefore, it was selected as the target strain. Molecular networking analysis via the Global Natural Products Social Molecular Networking (GNPS) platform identified 25 flavonoid compounds as flavonoid secondary metabolites. Among these, genistein was purified and identified as a bioactive compound with significant antibacterial activity. The complete synthesis pathway for genistein was proposed within strain B1075 based on whole-genome sequencing data, with the key gene being CHS (encoding chalcone synthase). The expression of the gene CHS was significantly regulated by high hydrostatic pressure, with a consequent impact on the production of flavonoid compounds in strain B1075, revealing the relationship between actinomycetes' synthesis of flavonoid-like secondary metabolites and their adaptation to high-pressure environments at the molecular level. These results not only expand our understanding of deep-sea microorganisms but also hold promise for providing valuable insights into the development of novel pharmaceuticals in the field of biopharmaceuticals.
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Affiliation(s)
- Xin Li
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.C.); (W.W.); (J.F.)
| | - Yukun Cui
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.C.); (W.W.); (J.F.)
| | - Weichao Wu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.C.); (W.W.); (J.F.)
| | - Zhizhen Zhang
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China;
| | - Jiasong Fang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.C.); (W.W.); (J.F.)
| | - Xi Yu
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.C.); (W.W.); (J.F.)
| | - Junwei Cao
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai 201306, China; (X.L.); (Y.C.); (W.W.); (J.F.)
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Ribeiro I, Correia S, Blümel M, Albuquerque P, Gorb SN, Mendes MV, Tasdemir D, Mucha AP, Carvalho MF. Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal. Int J Syst Evol Microbiol 2024; 74. [PMID: 38639738 DOI: 10.1099/ijsem.0.006341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
A novel strain, MA3_2.13T, was isolated from deep-sea sediment of Madeira Archipelago, Portugal, and characterized using a polyphasic approach. This strain produced dark brown soluble pigments, bronwish black substrate mycelia and an aerial mycelium with yellowish white spores, when grown on GYM 50SW agar. The main respiratory quinones were MK-10(H4), MK-10(H6) and MK-10(H8). Diphosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two glycophospholipids were identified as the main phospholipids. The major cellular fatty acids were iso-C16 : 1, iso-C16 : 0, anteiso-C17 : 1 and anteiso-C17 : 0. Phylogenetic analyses based on 16S rRNA gene showed that strain MA3_2.13T is a member of the genus Streptomyces and was most closely related to Streptomyces triticirhizae NEAU-YY642T (NR_180032.1; 16S rRNA gene similarity 97.9 %), Streptomyces sedi YIM 65188T (NR_044582.1; 16S rRNA gene similarity 97.4 %), Streptomyces mimosae 3MP-10T (NR_170412.1; 16S rRNA gene similarity 97.3 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (NR_133874.1; 16S rRNA gene similarity 97.0 %). Genome pairwise comparisons with closest related type strains retrieved values below the threshold for species delineation suggesting that strain MA3_2.13T represents a new branch within the genus Streptomyces. Based on these results, strain MA3_2.13T (=DSM 115980T=LMG 33094T) is proposed as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces profundus sp. nov. is proposed.
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Affiliation(s)
- Inês Ribeiro
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Sofia Correia
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Pedro Albuquerque
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
- IBMC - Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Stanislav N Gorb
- Functional Morphology and Biomechanics, Zoological Institute, Kiel University, Kiel, Germany
| | - Marta V Mendes
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
- IBMC - Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Kiel University, Kiel, Germany
| | - Ana P Mucha
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- FCUP - Faculty of Sciences of the University of Porto, Porto, Portugal
| | - Maria F Carvalho
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research,University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
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Barzkar N, Sukhikh S, Babich O. Study of marine microorganism metabolites: new resources for bioactive natural products. Front Microbiol 2024; 14:1285902. [PMID: 38260902 PMCID: PMC10800913 DOI: 10.3389/fmicb.2023.1285902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/04/2023] [Indexed: 01/24/2024] Open
Abstract
The marine environment has remained a source of novel biological molecules with diversified applications. The ecological and biological diversity, along with a unique physical environment, have provided the evolutionary advantage to the plant, animals and microbial species thriving in the marine ecosystem. In light of the fact that marine microorganisms frequently interact symbiotically or mutualistically with higher species including corals, fish, sponges, and algae, this paper intends to examine the potential of marine microorganisms as a niche for marine bacteria. This review aims to analyze and summarize modern literature data on the biotechnological potential of marine fungi and bacteria as producers of a wide range of practically valuable products (surfactants, glyco-and lipopeptides, exopolysaccharides, enzymes, and metabolites with different biological activities: antimicrobial, antitumor, and cytotoxic). Hence, the study on bioactive secondary metabolites from marine microorganisms is the need of the hour. The scientific novelty of the study lies in the fact that for the first time, the data on new resources for obtaining biologically active natural products - metabolites of marine bacteria and fungi - were generalized. The review investigates the various kinds of natural products derived from marine microorganisms, specifically focusing on marine bacteria and fungi as a valuable source for new natural products. It provides a summary of the data regarding the antibacterial, antimalarial, anticarcinogenic, antibiofilm, and anti-inflammatory effects demonstrated by marine microorganisms. There is currently a great need for scientific and applied research on bioactive secondary metabolites of marine microorganisms from the standpoint of human and animal health.
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Affiliation(s)
- Noora Barzkar
- Department of Agro-Industrial Technology, Faculty of Applied Science, Food and Agro-Industrial Research Center, King Mongkut’s University of Technology North Bangkok, Bangkok, Thailand
| | - Stanislav Sukhikh
- Research and Education Center “Industrial Biotechnologies”, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Olga Babich
- Research and Education Center “Industrial Biotechnologies”, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
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Freyria NJ, Góngora E, Greer CW, Whyte LG. High Arctic seawater and coastal soil microbiome co-occurrence and composition structure and their potential hydrocarbon biodegradation. ISME COMMUNICATIONS 2024; 4:ycae100. [PMID: 39101031 PMCID: PMC11296632 DOI: 10.1093/ismeco/ycae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/18/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
The accelerated decline in Arctic sea-ice cover and duration is enabling the opening of Arctic marine passages and improving access to natural resources. The increasing accessibility to navigation and resource exploration and production brings risks of accidental hydrocarbon releases into Arctic waters, posing a major threat to Arctic marine ecosystems where oil may persist for many years, especially in beach sediment. The composition and response of the microbial community to oil contamination on Arctic beaches remain poorly understood. To address this, we analyzed microbial community structure and identified hydrocarbon degradation genes among the Northwest Passage intertidal beach sediments and shoreline seawater from five high Arctic beaches. Our results from 16S/18S rRNA genes, long-read metagenomes, and metagenome-assembled genomes reveal the composition and metabolic capabilities of the hydrocarbon microbial degrader community, as well as tight cross-habitat and cross-kingdom interactions dominated by lineages that are common and often dominant in the polar coastal habitat, but distinct from petroleum hydrocarbon-contaminated sites. In the polar beach sediment habitats, Granulosicoccus sp. and Cyclocasticus sp. were major potential hydrocarbon-degraders, and our metagenomes revealed a small proportion of microalgae and algal viruses possessing key hydrocarbon biodegradative genes. This research demonstrates that Arctic beach sediment and marine microbial communities possess the ability for hydrocarbon natural attenuation. The findings provide new insights into the viral and microalgal communities possessing hydrocarbon degradation genes and might represent an important contribution to the removal of hydrocarbons under harsh environmental conditions in a pristine, cold, and oil-free environment that is threatened by oil spills.
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Affiliation(s)
- Nastasia J Freyria
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Esteban Góngora
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
- Energy, Mining and Environment, Research Centre, National Research Council Canada, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
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Delbari Y, Mohassel Y, Kakaei E, Bahrami Y. Identification and anti-bacterial property of endophytic actinobacteria from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa. Sci Rep 2023; 13:13145. [PMID: 37573468 PMCID: PMC10423286 DOI: 10.1038/s41598-023-40478-x] [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: 03/29/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023] Open
Abstract
The arbitrary and overuses of antibiotics have resulted in the emergence of multidrug resistance bacteria which encounters human to a serious public health problem. Thus, there is an ever-increasing demand for discovery of novel effective antibiotics with new modes of function against resistant pathogens. Endophytic actinobacteria (EA) have currently been considered as one of the most prospective group of microorganisms for discovery of therapeutic agents. This study aimed to isolate EA from Thymes kotschyanus, Allium hooshidaryae, and Cerasus microcarpa plants and to evaluate their antibacterial properties. The healthy samples were collected, dissected and surface-sterilized before cultured on four different selection media at 28 °C. Nine EA were isolated and identified based on morphological and molecular properties, and scanning electron micrograph analyses. Based on phylogenetic analysis, they were taxonomically grouped into four families Streptomycetaceae, Nocardiaceae, Micromonosporaceae, and Pseudonocardiaceae. Their branched aerial mycelia produced chains of cylindrical or cube or oval shaped spores with smooth or rough surfaces. Four strains; IKBG03, IKBG05, IKBG13, and IKBG17 had less than 98.65% sequence similarity to their closely related strains, which constitute them as novel species/strains. Besides, three strains; IKBG05, IKBG13, and IKBG18 were reported as endophytes for the first time. Preliminary antibacterial activity conducted on the all isolates revealed potent antibacterial effects against Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. All isolates strongly inhibited the growth of at least one of the tested pathogens. Our results reveals that the test plants are novel sources for isolating a diverse group of rare and common actinobacteria that could produce a wide range of novel biologically active natural products with antibacterial activity which have a great potential in pharmaceutical and biotechnological applications.
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Affiliation(s)
- Yaser Delbari
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yaser Mohassel
- Department of Clinical Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Elham Kakaei
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yadollah Bahrami
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Department of Medical Biotechnology, School of Medicine, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
- Advanced Marine Biomanufacturing Laboratory, Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, SA, 5042, Australia.
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