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Gignoux-Wolfsohn S, Garcia Ruiz M, Portugal Barron D, Ruiz G, Lohan K. Bivalve microbiomes are shaped by host species, size, parasite infection, and environment. PeerJ 2024; 12:e18082. [PMID: 39399422 PMCID: PMC11468899 DOI: 10.7717/peerj.18082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 08/20/2024] [Indexed: 10/15/2024] Open
Abstract
Many factors affect an organism's microbiome including its environment, proximity to other organisms, and physiological condition. As filter feeders, bivalves have highly plastic microbiomes that are especially influenced by the surrounding seawater, yet they also maintain a unique core set of microbes. Using 16S ribosomal RNA sequencing, we characterized the bacterial microbiomes of four species of bivalves native to the Mid-Atlantic East Coast of North America: Crassostrea virginica, Macoma balthica, Ameritella mitchelli, and Ischadium recurvum and assessed the impact of their external environment, internal parasites, and size on their microbial communities. We found significant differences in bacterial amplicon sequence variants (ASVs) across species, with each species harboring a core ASV present across all individuals. We further found that some C. virginica co-cultured with I. recurvum had high abundances of the I. recurvum core ASV. We identified ASVs associated with infection by the parasites Perkinsus marinus and Zaops ostreum as well others associated with bivalve size. Several of these ASV are candidates for further investigation as potential probiotics, as they were found positively correlated with bivalve size and health. This research represents the first description of the microbiomes of A. mitchelli, I. recurvum, and M. balthica. We document that all four species have highly plastic microbiomes, while maintaining certain core bacteria, with important implications for growth, health, and adaptation to new environments.
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Affiliation(s)
- Sarah Gignoux-Wolfsohn
- Biological Sciences, University of Massachusetts at Lowell, Lowell, MA, United States
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
| | - Monserrat Garcia Ruiz
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
| | - Diana Portugal Barron
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
- Department of Neurology, Brain Research Institute, Mary S. Easton Center for Alzheimer’s Research and Care, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gregory Ruiz
- Marine Invasions Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
| | - Katrina Lohan
- Coastal Disease Ecology Laboratory, Smithsonian Environmental Research Center, Edgewater, MD, United States
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2
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Ghezzi D, Salvi L, Costantini PE, Firrincieli A, Iorio M, Lopo E, Sosio M, Elbanna AH, Khalil ZG, Capon RJ, De Waele J, Vergara F, Sauro F, Cappelletti M. Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential. Microbiol Res 2024; 286:127793. [PMID: 38901277 DOI: 10.1016/j.micres.2024.127793] [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] [Received: 02/02/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Luca Salvi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Paolo E Costantini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo 01100, Italy
| | | | - Ettore Lopo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | | | - Ahmed H Elbanna
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Department of Pharmacognosy, Cairo University, Cairo 11562, Egypt
| | - Zeinab G Khalil
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jo De Waele
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Freddy Vergara
- La Venta Geographic Explorations Association, Treviso 31100, Italy; Teraphosa Exploring Team, Puerto Ordaz, Venezuela
| | - Francesco Sauro
- La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy.
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Hu P, Sharaby Y, Gu J, Radian A, Lang‐Yona N. Environmental processes and health implications potentially mediated by dust-borne bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13222. [PMID: 38151778 PMCID: PMC10866058 DOI: 10.1111/1758-2229.13222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023]
Abstract
Understanding microbial migration and survival mechanisms in dust events (DEs) can elucidate genetic and metabolic exchange between environments and help predict the atmospheric pathways of ecological and health-related microbial stressors. Dust-borne microbial communities have been previously characterized, but the impact and interactions between potentially active bacteria within transported communities remain limited. Here, we analysed samples collected during DEs in Israel, using amplicon sequencing of the 16S rRNA genes and transcripts. Different air trajectories and wind speeds were associated not only with the genomic microbial community composition variations but also with specific 16S rRNA bacterial transcripts. Potentially active dust-borne bacteria exhibited positive interactions, including carbon and nitrogen cycling, biotransformation of heavy metals, degradation of organic compounds, biofilm formation, and the presence of pathogenic taxa. This study provides insights into the potential interactive relationships and survival strategies of microorganisms within the extreme dust environment.
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Affiliation(s)
- Pengfei Hu
- Civil and Environmental EngineeringTechnion—Israel Institute of TechnologyHaifaIsrael
- Environmental Science and Engineering Research GroupGuangdong Technion—Israel Institute of TechnologyShantouGuangdongChina
| | - Yehonatan Sharaby
- Civil and Environmental EngineeringTechnion—Israel Institute of TechnologyHaifaIsrael
- Present address:
Department of Biology and EnvironmentUniversity of HaifaOranimTivonIsrael
| | - Ji‐Dong Gu
- Environmental Science and Engineering Research GroupGuangdong Technion—Israel Institute of TechnologyShantouGuangdongChina
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy ConversionGuangdong Technion—Israel Institute of TechnologyShantouGuangdongChina
| | - Adi Radian
- Civil and Environmental EngineeringTechnion—Israel Institute of TechnologyHaifaIsrael
| | - Naama Lang‐Yona
- Civil and Environmental EngineeringTechnion—Israel Institute of TechnologyHaifaIsrael
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Núñez-Montero K, Rojas-Villalta D, Barrientos L. Antarctic Sphingomonas sp. So64.6b showed evolutive divergence within its genus, including new biosynthetic gene clusters. Front Microbiol 2022; 13:1007225. [DOI: 10.3389/fmicb.2022.1007225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022] Open
Abstract
IntroductionThe antibiotic crisis is a major human health problem. Bioprospecting screenings suggest that proteobacteria and other extremophile microorganisms have biosynthetic potential for the production novel antimicrobial compounds. An Antarctic Sphingomonas strain (So64.6b) previously showed interesting antibiotic activity and elicitation response, then a relationship between environmental adaptations and its biosynthetic potential was hypothesized. We aimed to determine the genomic characteristics in So64.6b strain related to evolutive traits for the adaptation to the Antarctic environment that could lead to its diversity of potentially novel antibiotic metabolites.MethodsThe complete genome sequence of the Antarctic strain was obtained and mined for Biosynthetic Gene Clusters (BGCs) and other unique genes related to adaptation to extreme environments. Comparative genome analysis based on multi-locus phylogenomics, BGC phylogeny, and pangenomics were conducted within the closest genus, aiming to determine the taxonomic affiliation and differential characteristics of the Antarctic strain.Results and discussionThe Antarctic strain So64.6b showed a closest identity with Sphingomonas alpina, however containing a significant genomic difference of ortholog cluster related to degradation multiple pollutants. Strain So64.6b had a total of six BGC, which were predicted with low to no similarity with other reported clusters; three were associated with potential novel antibiotic compounds using ARTS tool. Phylogenetic and synteny analysis of a common BGC showed great diversity between Sphingomonas genus but grouping in clades according to similar isolation environments, suggesting an evolution of BGCs that could be linked to the specific ecosystems. Comparative genomic analysis also showed that Sphingomonas species isolated from extreme environments had the greatest number of predicted BGCs and a higher percentage of genetic content devoted to BGCs than the isolates from mesophilic environments. In addition, some extreme-exclusive clusters were found related to oxidative and thermal stress adaptations, while pangenome analysis showed unique resistance genes on the Antarctic strain included in genetic islands. Altogether, our results showed the unique genetic content on Antarctic strain Sphingomonas sp. So64.6, −a probable new species of this genetically divergent genus–, which could have potentially novel antibiotic compounds acquired to cope with Antarctic poly-extreme conditions.
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Stonik VA, Makarieva TN, Shubina LK. Antibiotics from Marine Bacteria. BIOCHEMISTRY (MOSCOW) 2021; 85:1362-1373. [PMID: 33280579 DOI: 10.1134/s0006297920110073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This review discusses main directions and results of the studies on antibiotics produced by bacteria living in the marine environment. In recent years many obligate marine species and strains were studied, diverse metabolites were isolated, and their chemical structures were elucidated. Among them here were natural compounds toxic against tumor cells, pathogenic bacteria, viruses, and malaria plasmodial species; these compounds often had no analogues among the natural products of terrestrial origin. Some isolated compounds form a basis of active ingredients in medicinal preparations used in clinic practice, while others are under different stages of preclinical or clinical studies. Much attention has been paid in recent years to producers of marine-derived antibiotics isolated from the deep-sea habitats, from the surface of marine invertebrates and algae, as well as from symbiotic microorganisms.
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Affiliation(s)
- V A Stonik
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences (PIBOC), Vladivostok, 690022, Russia.
| | - T N Makarieva
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences (PIBOC), Vladivostok, 690022, Russia
| | - L K Shubina
- Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences (PIBOC), Vladivostok, 690022, Russia
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The bacterial and fungal nest microbiomes in populations of the social spider Stegodyphus dumicola. Syst Appl Microbiol 2021; 44:126222. [PMID: 34146923 DOI: 10.1016/j.syapm.2021.126222] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/09/2021] [Accepted: 05/26/2021] [Indexed: 12/17/2022]
Abstract
Social spiders of the species Stegodyphus dumicola live in communal nests with hundreds of individuals and are characterized by extremely low species-wide genetic diversity. The lack of genetic diversity in combination with group living imposes a potential threat for infection by pathogens. We therefore proposed that specific microbial symbionts inhabiting the spider nests may provide antimicrobial defense. To compare the bacterial and fungal diversity in 17 nests from three different locations in Namibia, we used 16S rRNA gene and internal transcribed spacer (ITS2) sequencing. The nest microbiomes differed between geographically distinct spider populations and appeared largely determined by the local environment. Nevertheless, we identified a core microbiome consisting of four bacterial genera (Curtobacterium, Modestobacter, Sphingomonas, Massilia) and four fungal genera (Aureobasidium, Didymella, Alternaria, Ascochyta), which likely are selected from surrounding soil and plants by the nest environment. We did not find indications for a strain- or species-specific symbiosis in the nests. Isolation of bacteria and fungi from nest material retrieved a few bacterial strains with antimicrobial activity but a number of antimicrobial fungi, including members of the fungal core microbiome. The significance of antimicrobial taxa in the nest microbiome for host protection remains to be shown.
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Yang S, Li X, Xiao X, Zhuang G, Zhang Y. Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench. Int J Syst Evol Microbiol 2020; 70:3809-3815. [PMID: 32496177 DOI: 10.1099/ijsem.0.004235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, short rod-shaped, yellow bacterium (strain LMO-1T) was isolated from deep-sea sediment of the Mariana Trench, Challenger Deep. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LMO-1T belonged to genus Sphingomonas, with the highest sequence similarity to Sphingomonas formosensis CC-Nfb-2T (96.3 %), followed by Sphingomonas prati W18RDT (96.1 %), Sphingomonas arantia 6PT (96.0 %) and Sphingomonas montana W16RDT (95.9 %). The predominant polar lipids were phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol and phosphatidylcholine. The main cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C14 : 0 2-OH. The major polyamine was sym-homospermidine and the predominant isoprenoid quinone was ubiquinone-10. The genome DNA G+C content of strain LMO-1T was 69.2 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LMO-1T and CC-Nfb-2T were 75.9 and 20.5 %, respectively. Based on these data, LMO-1T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas profundi sp. nov. is proposed. The type strain is LMO-1T (=MCCC 1K04066T=JCM 33666T).
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Affiliation(s)
- Shanshan Yang
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China.,State Key Laboratory of Ocean Engineering, State Key Laboratory of Microbial Metabolism, Shanghai, PR China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xuegong Li
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, PR China
| | - Xiang Xiao
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China.,State Key Laboratory of Ocean Engineering, State Key Laboratory of Microbial Metabolism, Shanghai, PR China
| | - Guangjiao Zhuang
- State Key Laboratory of Ocean Engineering, State Key Laboratory of Microbial Metabolism, Shanghai, PR China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China.,State Key Laboratory of Ocean Engineering, State Key Laboratory of Microbial Metabolism, Shanghai, PR China
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Kim YJ, Park JY, Balusamy SR, Huo Y, Nong LK, Thi Le H, Yang DC, Kim D. Comprehensive Genome Analysis on the Novel Species Sphingomonas panacis DCY99 T Reveals Insights into Iron Tolerance of Ginseng. Int J Mol Sci 2020; 21:E2019. [PMID: 32188055 PMCID: PMC7139845 DOI: 10.3390/ijms21062019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 11/18/2022] Open
Abstract
Plant growth-promoting rhizobacteria play vital roles not only in plant growth, but also in reducing biotic/abiotic stress. Sphingomonas panacis DCY99T is isolated from soil and root of Panax ginseng with rusty root disease, characterized by raised reddish-brown root and this is seriously affects ginseng cultivation. To investigate the relationship between 159 sequenced Sphingomonas strains, pan-genome analysis was carried out, which suggested genomic diversity of the Sphingomonas genus. Comparative analysis of S. panacis DCY99T with Sphingomonas sp. LK11 revealed plant growth-promoting potential of S. panacis DCY99T through indole acetic acid production, phosphate solubilizing, and antifungal abilities. Detailed genomic analysis has shown that S. panacis DCY99T contain various heavy metals resistance genes in its genome and the plasmid. Functional analysis with Sphingomonas paucimobilis EPA505 predicted that S. panacis DCY99T possess genes for degradation of polyaromatic hydrocarbon and phenolic compounds in rusty-ginseng root. Interestingly, when primed ginseng with S. panacis DCY99T during high concentration of iron exposure, iron stress of ginseng was suppressed. In order to detect S. panacis DCY99T in soil, biomarker was designed using spt gene. This study brings new insights into the role of S. panacis DCY99T as a microbial inoculant to protect ginseng plants against rusty root disease.
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Affiliation(s)
- Yeon-Ju Kim
- College of Life Science, Kyung Hee University, Yongin 16710, Korea; (Y.H.); (D.C.Y.)
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea; (J.Y.P.); (L.K.N.); (H.T.L.)
| | | | - Yue Huo
- College of Life Science, Kyung Hee University, Yongin 16710, Korea; (Y.H.); (D.C.Y.)
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea; (J.Y.P.); (L.K.N.); (H.T.L.)
| | - Hoa Thi Le
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea; (J.Y.P.); (L.K.N.); (H.T.L.)
| | - Deok Chun Yang
- College of Life Science, Kyung Hee University, Yongin 16710, Korea; (Y.H.); (D.C.Y.)
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea; (J.Y.P.); (L.K.N.); (H.T.L.)
- School of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
- Korean Genomics Industrialization and Commercialization Center, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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Asaf S, Numan M, Khan AL, Al-Harrasi A. Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth. Crit Rev Biotechnol 2020; 40:138-152. [PMID: 31906737 DOI: 10.1080/07388551.2019.1709793] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actual biotechnological potential of this genus requires further assessment. Some of the species from the genus have also been noted to improve plant-growth during stress conditions such as drought, salinity, and heavy metals in agricultural soil. This role has been attributed to their potential to produce plant growth hormones e.g. gibberellins and indole acetic acid. However, the current literature is scattered, and some of the important areas, such as taxonomy, phylogenetics, genome mapping, and cellular transport systems, are still being overlooked in terms of elucidation of the mechanisms behind stress-tolerance and bioremediation. In this review, we elucidated the prospective role and function of this genus for improved utilization during environmental biotechnology.
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Affiliation(s)
- Sajjad Asaf
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Muhammad Numan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Abdul Latif Khan
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
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Cha I, Kang H, Kim H, Joh K. Sphingomonas ginkgonis sp. nov., isolated from phyllosphere of Ginkgo biloba. Int J Syst Evol Microbiol 2019; 69:3224-3229. [PMID: 31343398 DOI: 10.1099/ijsem.0.003613] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain HMF7854T, isolated from a ginkgo tree, was an orange-pigmented, Gram-stain-negative, motile by means of a single flagellum, strictly aerobic, rod-shaped bacterium. The isolate grew optimally on Reasoner's 2A agar at 30 °C, pH 7.0-8.0 and 0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HMF7854T belonged to the genus Sphingomonas and was most closely related to Sphingomonasagri HKS-06T (96.8 % sequence similarity). The major fatty acids were C17 : 1 ω6c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The predominant isoprenoid quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 68.4 mol%. Thus, based on its phylogenetic, phenotypic and chemotaxonomic data, strain HMF7854T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasginkgonis sp. nov. is proposed. The type strain of the species is strain HMF7854T (=KCTC 62461T=NBRC 113337T).
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Affiliation(s)
- Inseong Cha
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Heeyoung Kang
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Haneul Kim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
| | - Kiseong Joh
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Republic of Korea
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11
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Romanenko LA, Kurilenko VV, Guzev KV, Svetashev VI. Characterization of Labrenzia polysiphoniae sp. nov. isolated from red alga Polysiphonia sp. Arch Microbiol 2019; 201:705-712. [DOI: 10.1007/s00203-019-01640-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/21/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
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Gómez-Acata S, Vital-Jácome M, Pérez-Sandoval MV, Navarro-Noya YE, Thalasso F, Luna-Guido M, Conde-Barajas E, Dendooven L. Microbial community structure in aerobic and fluffy granules formed in a sequencing batch reactor supplied with 4-chlorophenol at different settling times. JOURNAL OF HAZARDOUS MATERIALS 2018; 342:606-616. [PMID: 28898858 DOI: 10.1016/j.jhazmat.2017.08.073] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 06/07/2023]
Abstract
Toxic compounds, such as 4-chlorophenol (4-CP), which is a common pollutant in wastewater, are removed efficiently from sequencing batch reactors (SBRs) by microorganisms. The bacterial community in aerobic granules formed during the removal of 4-CP in a SBR was monitored for 63days. The SBR reactor was operated with a constant filling and withdrawal time of 7 and 8min and decreasing settling time (30, 5, 3 and 2min) to induce the formation of aerobic granules. During the acclimation period lasting 15days (30min settling time) had a strong effect on the bacterial community. From day 18 onwards, Sphingobium and Comamonadaceae were detected. Rhizobiaceae were dominant from day 24 to day 28 when stable aerobic granules were formed. At day 35, fluffy granules were formed, but the bacterial community structure did not change, despite the changes in the reactor operation to inhibit filamentous bacteria growth. This is the first report on changes in the bacterial community structure of aerobic and fluffy granules during granulation process in a reactor fed with 4-CP and the prediction of its metabolic pathways.
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Affiliation(s)
- Selene Gómez-Acata
- Department of Environmental Engineering, Instituto Tecnológico de Celaya, Guanajuato, Mexico
| | | | | | | | | | - Marco Luna-Guido
- Laboratory of Soil Ecology, ABACUS, Cinvestav, México, D.F., Mexico
| | - Eloy Conde-Barajas
- Department of Environmental Engineering, Instituto Tecnológico de Celaya, Guanajuato, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, Cinvestav, México, D.F., Mexico.
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13
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Huang Y, Wei Z, Danzeng W, Kim MC, Zhu G, Zhang Y, Liu Z, Peng F. Sphingomonas antarctica sp. nov., isolated from Antarctic tundra soil. Int J Syst Evol Microbiol 2017; 67:4064-4068. [PMID: 28933318 DOI: 10.1099/ijsem.0.002253] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain 200T, isolated from a soil sample taken from Antarctic tundra soil around Zhongshan Station, was found to be a Gram-stain-negative, yellow-pigmented, catalase-positive, oxidase-negative, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain 200T grew optimally at pH 7.0 and in the absence of NaCl on R2A. Its optimum growth temperature was 20 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 200T belonged to the genus Sphingomonas. Strain 200T showed the highest sequence similarities to Sphingomonas kyeonggiense THG-DT81T (95.1 %) and Sphingomonas molluscorum KMM 3882T (95.1 %). Chemotaxonomic analysis showed that strain 200T had characteristics typical of members of the genus Sphingomonas. Ubiquinone 10 was the predominant respiratory quinone and sym-homospermidine was the polyamine. The major polar lipids were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The G+C content of the genomic DNA was determined to be 60.9 mol%. Strain 200T contained C16 : 0 (31.6 %), summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c, 22.7 %), summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 11.2 %), C18 : 0 (7.8 %) and C14 : 0 2OH (6.7 %) as the major cellular fatty acids. On the basis of phylogenetic analysis, and physiological and biochemical characterization, strain 200T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonasantarctica sp. nov. is proposed. The type strain is 200T (=CCTCC AB 2016064T=KCTC 52488T).
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Affiliation(s)
- Yao Huang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Ziyan Wei
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Wangmu Danzeng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Myong Chol Kim
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China.,College of Life Sciences, Kim II Sung University, Pyongyang, DPR of Korea
| | - Guoxin Zhu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yumin Zhang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zuobing Liu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fang Peng
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan 430072, PR China.,China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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Lee JH, Kim DI, Choe HN, Lee SD, Seong CN. Sphingomonas limnosediminicola sp. nov. and Sphingomonas palustris sp. nov., isolated from freshwater environments. Int J Syst Evol Microbiol 2017; 67:2834-2841. [DOI: 10.1099/ijsem.0.002029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Han Na Choe
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Soon Dong Lee
- Faculty of Science Education, Jeju National University, Jeju63243, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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Ko Y, Hwang WM, Kim M, Kang K, Ahn TY. Sphingomonas silvisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2017; 67:2704-2710. [DOI: 10.1099/ijsem.0.002001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yongseok Ko
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Woon Mo Hwang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Minsun Kim
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Tae-Young Ahn
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
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Sphingomonas montana sp. nov., isolated from a soil sample from the Tanggula Mountain in the Qinghai Tibetan Plateau. Antonie van Leeuwenhoek 2017; 110:1659-1668. [PMID: 28755311 DOI: 10.1007/s10482-017-0915-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
An orange pigmented, Gram-staining negative, aerobic, motile, rod-shaped bacterium isolated from a soil from the Tanggula Mountain, China was studied using a polyphasic approach. Based on 16S rRNA gene sequence similarity, strain W16RDT was found to be closely related to Sphingomonas prati DSM 103336T (99%), Sphingomonas fennica DSM 13665T (97.21%), followed by Sphingomonas laterariae DSM 25432T (96.44%), Sphingomonas haloaromaticamans CGMCC 1.10206 T (96.36%) and Sphingomonas formosensis DSM 24164T (96.06%). The strain was found to be catalase and oxidase positive and was found to grow optimally at temperatures of 20-25 °C, pH 8 and tolerated NaCl concentration up to 1% (w/v). The major fatty acids identified were summed feature eight comprising C18:1 ω 7c and/or C18:1 ω 6c (39.2%), summed feature three comprising of C16:1 ω7c and/or C16:1 ω6c (36.7%) and C16:0 (7.0%). The polar lipids detected were phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, and three unidentified lipids. The strain possessed ubiquinone-10 (Q-10) as the predominant respiratory quinone. Along with other distinguishing characteristics, we also describe the draft genome of strain W16RDT. The final assembled draft genome sequence is 3,722,743 bp with 3390 coding and 48 RNA (45 tRNA and 3 rRNA) genes. The DNA G+C content of the genomic DNA was determined to be 67%. The DNA-DNA relatedness value between the strain W16RDT and its closest phylogenetic relatives S. prati DSM 103336T, S. fennica DSM 13665T, S. laterariae DSM 25432T, and S. haloaromaticamans CGMCC 1.10206T were 52.17, 47.60, 20.93 and 17.09% respectively. The strain W16RDT could be distinguished genotypically and phenotypically from the recognized species belonging to the genus Sphingomonas and thus represents a novel species, for which the name Sphingomonas montana sp. nov. is proposed. The type strain is W16RDT (=CGMCC 1.15646T = DSM 103337T).
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Lee JH, Kim DI, Kang JW, Seong CN. Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir. Int J Syst Evol Microbiol 2016; 66:5493-5499. [DOI: 10.1099/ijsem.0.001546] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ji Hee Lee
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Dae In Kim
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Joo Won Kang
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea
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Liu D, Jin X, Sun X, Song Y, Feng L, Wang G, Li M. Sphingomonas faucium sp. nov., isolated from canyon soil. Int J Syst Evol Microbiol 2016; 66:2847-2852. [DOI: 10.1099/ijsem.0.001064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dongmei Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xin Jin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xuelian Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yali Song
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Liling Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Mingshun Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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Mageswari A, Subramanian P, Srinivasan R, Karthikeyan S, Gothandam KM. Astaxanthin from psychrotrophic Sphingomonas faeni exhibits antagonism against food-spoilage bacteria at low temperatures. Microbiol Res 2015; 179:38-44. [DOI: 10.1016/j.micres.2015.06.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/20/2015] [Accepted: 06/22/2015] [Indexed: 11/16/2022]
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20
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Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench). J Microbiol Methods 2015; 112:104-17. [DOI: 10.1016/j.mimet.2015.03.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 03/12/2015] [Accepted: 03/12/2015] [Indexed: 01/08/2023]
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21
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Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NI, Mikhailov VV. Rheinheimera japonica sp. nov., a novel bacterium with antimicrobial activity from seashore sediments of the Sea of Japan. Arch Microbiol 2015; 197:613-20. [DOI: 10.1007/s00203-015-1095-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 11/30/2022]
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22
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Zhu L, Si M, Li C, Xin K, Chen C, Shi X, Huang R, Zhao L, Shen X, Zhang L. Sphingomonas gei sp. nov., isolated from roots of Geum aleppicum. Int J Syst Evol Microbiol 2015; 65:1160-1166. [PMID: 25604345 DOI: 10.1099/ijs.0.000074] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow-pigmented bacterium, designated strain ZFGT-11(T), was isolated from roots of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China, and was subjected to a taxonomic study by using a polyphasic approach. Cells of strain ZFGT-11(T) were Gram-stain-negative, strictly aerobic rods that were surrounded by a thick capsule and were motile by means of a single polar flagellum. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFGT-11(T) was a member of the genus Sphingomonas and was closely related to Sphingomonas naasensis KACC 16534(T) (97.6% similarity), Sphingomonas kyeonggiense JCM 18825(T) (96.8%), Sphingomonas asaccharolytica IFO 15499(T) (96.7%) and Sphingomonas leidyi DSM 4733(T) (96.6%). The predominant respiratory quinone was ubiquinone-10 (Q-10) and the major cellular fatty acids were summed feature 8 (comprising C(18 : 1)ω7c and/or C(18 : 1)ω6c), C(17 : 1)ω6c, C(14 : 0) 2-OH, C(16 : 0) and C(15 : 0) 2-OH. The major polyamine of strain ZFGT-11(T) was sym-homospermidine. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, sphingoglycolipid, two unidentified aminoglycolipids, two unidentified phospholipids and two unidentified lipids were detected in the polar lipid profile. The DNA G+C content was 66.8 mol%. DNA-DNA relatedness for strain ZFGT-11(T) with respect to its closest phylogenetic relative S. naasensis KACC 16534(T) was 26.2±4.8% (mean±SD). On the basis of data from the present polyphasic taxonomic study, strain ZFGT-11(T) is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas gei sp. nov. is proposed. The type strain is ZFGT-11(T) ( = CCTCC AB 2013306(T) = KCTC 32449(T) = LMG 27608(T)).
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Affiliation(s)
- Lingfang Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Meiru Si
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Changfu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Kaiyun Xin
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chaoqiong Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xu Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Ruijun Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Liang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, PR China
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El Amraoui B, El Amraoui M, Cohen N, Fassouane A. Anti-Candida and anti-Cryptococcus antifungal produced by marine microorganisms. J Mycol Med 2014; 24:e149-53. [PMID: 25442916 DOI: 10.1016/j.mycmed.2014.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 04/20/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022]
Abstract
In order to search for antifungal from biological origin, we performed a screening of marine microorganisms isolated from seawater, seaweed, sediment and marine invertebrates collected from different coastal areas of the Moroccan Atlantic Ocean. The antifungal activities of these isolates were investigated against the pathogenic yeasts involved in medical mycology. Whole cultures of 34 marine microorganisms were screened for antifungal activities using the method of agar diffusion against four yeasts. The results showed that among the 34 isolates studied, 13 (38%) strains have antifungal activity against at least one out of four yeast species, 11 isolates have anti-Candida albicans CIP 48.72 activity, 12 isolates have anti-C. albicans CIP 884.65 activity, 13 isolates have anti-Cryptococcus neoformans activity and only 6 isolates are actives against Candida tropicalis R2 resistant to nystatin and amphotericin B. Nine isolates showed strong fungicidal activity. Fourteen microorganisms were identified and assigned to the genera Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Chromobacterium, Enterococcus, Pantoea, and Pseudomonas. Due to a competitive role for space and nutrient, the marine microorganisms could produce more antimicrobials; therefore these marine microorganisms were expected to be potential resources of natural products such as those we research: anti-Candida and anti-Cryptococcus fungicides.
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Affiliation(s)
- B El Amraoui
- Laboratoire de contrôle qualité en bio-industrie et molécules bioactives, faculté des sciences, université Chouaib Doukkali, BP 20, 24000 El Jadida, Morocco; Faculté polidisciplinaire, université Ibn Zohr, BP 271, 83000 Taroudant, Morocco.
| | - M El Amraoui
- Laboratoire de contrôle qualité en bio-industrie et molécules bioactives, faculté des sciences, université Chouaib Doukkali, BP 20, 24000 El Jadida, Morocco
| | - N Cohen
- Institut pasteur, microbiologie des aliments et de l'environnement, Casablanca, Morocco
| | - A Fassouane
- Laboratoire de contrôle qualité en bio-industrie et molécules bioactives, faculté des sciences, université Chouaib Doukkali, BP 20, 24000 El Jadida, Morocco
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Antifungal and antibacterial activity of marine microorganisms. ANNALES PHARMACEUTIQUES FRANÇAISES 2014; 72:107-11. [DOI: 10.1016/j.pharma.2013.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 11/27/2013] [Accepted: 12/02/2013] [Indexed: 11/15/2022]
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25
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Paenibacillus profundus sp. nov., a deep sediment bacterium that produces isocoumarin and peptide antibiotics. Arch Microbiol 2013; 195:247-54. [DOI: 10.1007/s00203-013-0873-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 12/08/2012] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
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26
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Antimicrobial potential of deep surface sediment associated bacteria from the Sea of Japan. World J Microbiol Biotechnol 2013; 29:1169-77. [DOI: 10.1007/s11274-013-1276-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/30/2013] [Indexed: 01/08/2023]
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27
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Tabares P, Pimentel-Elardo SM, Schirmeister T, Hünig T, Hentschel U. Anti-protease and immunomodulatory activities of bacteria associated with Caribbean sponges. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:883-892. [PMID: 21222136 PMCID: PMC7088305 DOI: 10.1007/s10126-010-9349-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 12/20/2010] [Indexed: 05/30/2023]
Abstract
Marine sponges and their associated bacteria have been proven to be a rich source of novel secondary metabolites with therapeutic usefulness in cancer, infection, and autoimmunity. In this study, 79 strains belonging to 20 genera of the order Actinomycetales and seven strains belonging to two genera of the order Sphingomonadales were cultivated from 18 different Caribbean sponges and identified by 16S rRNA gene sequencing. Seven of these strains are likely to represent novel species. Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. These results highlight the significance of marine sponge-associated bacteria to produce bioactive secondary metabolites with therapeutic potential in the treatment of infectious diseases and disorders of the immune system.
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Affiliation(s)
- Paula Tabares
- Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Sheila M. Pimentel-Elardo
- Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
| | - Tanja Schirmeister
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Thomas Hünig
- Institute for Virology and Immunobiology, University of Würzburg, Versbacherstr. 7, 97078 Würzburg, Germany
| | - Ute Hentschel
- Julius-von-Sachs-Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, 97082 Würzburg, Germany
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Park S, Yokota A, Itoh T, Park JS. Sphingomonas jejuensis sp. nov., isolated from marine sponge Hymeniacidon flavia. J Microbiol 2011; 49:238-42. [DOI: 10.1007/s12275-011-0500-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 04/15/2011] [Indexed: 10/18/2022]
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Kalinovskaya NI, Romanenko LA, Irisawa T, Ermakova SP, Kalinovsky AI. Marine isolate Citricoccus sp. KMM 3890 as a source of a cyclic siderophore nocardamine with antitumor activity. Microbiol Res 2011; 166:654-61. [PMID: 21376551 DOI: 10.1016/j.micres.2011.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 01/19/2011] [Accepted: 01/29/2011] [Indexed: 11/30/2022]
Abstract
A novel actinobacterium, designated KMM 3890 was isolated from a bottom sediment sample collected from the Sakhalin shallow environment. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated strain KMM 3890 affiliation to the genus Citricoccus. In addition to its hemolytic activity, this strain exhibited inhibitory activity against Gram-positive bacteria. It was found that the marine isolate Citricoccus sp. KMM 3890 produced and excreted into the culture medium a large amount of the compound, which was isolated and structurally characterized as known cyclic siderophore nocardamine on the basis of combined spectral analyses. Nocardamine showed inhibitory effects to colony formation of T-47D, SK-Mel-5, SK-Mel-28 and PRMI-7951 tumor cell lines and a weak antimicrobial against Gram-positive bacteria and no revealed cytotoxic activity. This study can be considered as the first report on marine isolate of the genus Citricoccus producing nocardamine with antitumor activity.
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Affiliation(s)
- Nataliya I Kalinovskaya
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospect 100 Let Vladivostoku 159, Vladivostok, Russian Federation.
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30
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Zhang JY, Liu XY, Liu SJ. Sphingomonas changbaiensis sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2010; 60:790-795. [DOI: 10.1099/ijs.0.011486-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial strain V2M44Twas isolated from forest soil from the Changbai Mountains, Heilongjiang Province, China. Cells of strain V2M44Twere Gram-negative, rod-shaped and 0.3–0.4 μm in diameter and 1.5–2.5 μm long. The cells were strictly aerobic and were motile by means of peritrichous flagella. Growth occurred at 20–33 °C (optimum, 29–31 °C), at pH 5–8 (optimum, pH 6.0–7.0) and in the presence of 0−0.1 % (w/v) NaCl (optimum, 0.05 %). Strain V2M44Tcontained C17 : 1ω6c(38.9 %) and summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9tand/or C18 : 1ω12t, 31.5 %) as the major cellular fatty acids and Q-10 as the major respiratory quinone. The major polar lipids were sphingoglycolipid, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol along with two unidentified phospholipids and four unidentified glycolipids. The major component in the polyamine pattern wassym-homospermidine. The DNA G+C content was 65.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain V2M44Twas phylogenetically related to members of the genusSphingomonas, with sequence similarities ranging from 92.0–95.8 %. Based on these results, it is concluded that strain V2M44Trepresents a novel species of the genusSphingomonas, for which the nameSphingomonas changbaiensissp. nov. is proposed. The type strain is V2M44T(=CGMCC 1.7057T=NBRC 104936T).
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Affiliation(s)
- Jia-Yue Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Xing-Yu Liu
- National Engineering Laboratory of Biohydrometallurgy, General Research Institute for Nonferrous Metals, Beijing, 100088, PR China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
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Reynisson E, Lauzon HL, Magnússon H, Jónsdóttir R, Olafsdóttir G, Marteinsson V, Hreggvidsson GO. Bacterial composition and succession during storage of North-Atlantic cod (Gadus morhua) at superchilled temperatures. BMC Microbiol 2009; 9:250. [PMID: 19961579 PMCID: PMC2797803 DOI: 10.1186/1471-2180-9-250] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 12/04/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The bacteriology during storage of the North-Atlantic cod has been investigated for the past decades using conventional cultivation strategies which have generated large amount of information. This paper presents a study where both conventional cultivation and cultivation independent approaches were used to investigate the bacterial succession during storage of cod loins at chilled and superchilled temperatures. RESULTS Unbrined (0.4% NaCl) and brined (2.5% NaCl) cod loins were stored at chilled (0 degrees C) and superchilled (-2 and -3.6 degrees C) temperatures in air or modified atmosphere (MA, % CO2/O2/N2: 49.0 +/- 0.6/7.4 +/- 0.2/43.7 +/- 0.4). Discrepancy was observed between cultivation enumeration and culture independent methods where the former showed a general dominance of Pseudomonas spp. (up to 59%) while the latter showed a dominance of Photobacterium phosphoreum (up to 100%).Gas chromatography-mass spectrophotometry (GC-MC) showed that trimethylamine was the most abundant volatile in mid- and late storage periods. Terminal restriction polymorphism (t-RFLP) analysis showed that the relative abundance of P. phosphoreum increased with storage time. CONCLUSION The present study shows the bacteriological developments on lightly salted or non-salted cod loins during storage at superchilled temperatures. It furthermore confirms the importance of P. phosphoreum as a spoilage organism during storage of cod loins at low temperatures using molecular techniques. The methods used compensate each other, giving more detailed data on bacterial population developments during spoilage.
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Affiliation(s)
- Eyjólfur Reynisson
- Food Safety & Environment, Matis-Icelandic Food Research (Vínlandsleieth 12), Reykjavík, Iceland.
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Trindade-Silva AE, Machado-Ferreira E, Senra MVX, Vizzoni VF, Yparraguirre LA, Leoncini O, Soares CAG. Physiological traits of the symbiotic bacterium Teredinibacter turnerae isolated from the mangrove shipworm Neoteredo reynei. Genet Mol Biol 2009; 32:572-81. [PMID: 21637522 PMCID: PMC3036054 DOI: 10.1590/s1415-47572009005000061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 03/23/2009] [Indexed: 11/22/2022] Open
Abstract
Nutrition in the Teredinidae family of wood-boring mollusks is sustained by cellulolytic/nitrogen fixing symbiotic bacteria of the Teredinibacter clade. The mangrove Teredinidae Neoteredo reynei is popularly used in the treatment of infectious diseases in the north of Brazil. In the present work, the symbionts of N. reynei, which are strictly confined to the host's gills, were conclusively identified as Teredinibacter turnerae. Symbiont variants obtained in vitro were able to grow using casein as the sole carbon/nitrogen source and under reduced concentrations of NaCl. Furthermore, cellulose consumption in T. turnerae was clearly reduced under low salt concentrations. As a point of interest, we hereby report first hand that T. turnerae in fact exerts antibiotic activity. Furthermore, this activity was also affected by NaCl concentration. Finally, T. turnerae was able to inhibit the growth of Gram-negative and Gram-positive bacteria, this including strains of Sphingomonas sp., Stenotrophomonas maltophilia, Bacillus cereus and Staphylococcus sciuri. Our findings introduce new points of view on the ecology of T. turnerae, and suggest new biotechnological applications for this marine bacterium.
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Affiliation(s)
- Amaro E Trindade-Silva
- Laboratório de Genética Molecular de Eucariontes e Simbiontes, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ Brazil
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Romanenko LA, Tanaka N, Frolova GM. Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan. Int J Syst Evol Microbiol 2009; 60:603-609. [PMID: 19654350 DOI: 10.1099/ijs.0.010728-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, KMM 3891(T) and KMM 3892, were isolated from internal tissues of the marine mollusc Umbonium costatum collected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink-reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C(17 : 1)omega6c, C(17 : 0), C(16 : 0) and C(16 : 1)omega7c as the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891(T) was 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891(T) and KMM 3892 were positioned within the Gammaproteobacteria as a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives including Saccharophagus degradans, Microbulbifer species, Endozoicomonas elysicola, Simiduia agarivorans and Teredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891(T) and KMM 3892 represent a new genus and species, for which the name Umboniibacter marinipuniceus gen. nov., sp. nov. is proposed. The type strain of Umboniibacter marinipuniceus is KMM 3891(T) (=NRIC 0753(T) =JCM 15738(T)).
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Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Galina M Frolova
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia
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Yoon JH, Park S, Kang SJ, Kim W, Oh TK. Sphingomonas hankookensis sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 2009; 59:2788-93. [DOI: 10.1099/ijs.0.008680-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Huang HD, Wang W, Ma T, Li GQ, Liang FL, Liu RL. Sphingomonas sanxanigenens sp. nov., isolated from soil. Int J Syst Evol Microbiol 2009; 59:719-23. [PMID: 19329595 DOI: 10.1099/ijs.0.000257-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain NX02(T), a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil, and its taxonomic position was investigated using a polyphasic approach. Chemotaxonomic analysis revealed that strain NX02(T) possessed Q-10 as the predominant ubiquinone, sym-homospermidine as the major polyamine and C(18 : 1)omega7c, C(16 : 0) and C(14 : 0) 2-OH as the major fatty acids. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified glycolipid. The DNA G+C content was 66.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NX02(T) belongs to the alpha-4 subgroup of the Proteobacteria, exhibiting the highest sequence similarity with respect to Sphingomonas azotifigens NBRC 15497(T) (95.9 %), Sphingomonas pituitosa DSM 13101(T) (95.8 %) and Sphingomonas dokdonensis KCTC 12541(T) (95.8 %). On the basis of these results, strain NX02(T) represents a novel species of the genus Sphingomonas sensu stricto, for which the name Sphingomonas sanxanigenens sp. nov. is proposed. The type strain is NX02(T) (=DSM 19645(T) =CGMCC 1.6417(T)).
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Affiliation(s)
- Hai-Dong Huang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, PR China
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Romanenko LA, Tanaka N, Frolova GM, Mikhailov VV. Sphingomonas japonica sp. nov., isolated from the marine crustacean Paralithodes camtschatica. Int J Syst Evol Microbiol 2009; 59:1179-82. [DOI: 10.1099/ijs.0.003285-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Romanenko LA, Tanaka N, Uchino M, Kalinovskaya NI, Mikhailov VV. Diversity and Antagonistic Activity of Sea Ice Bacteria Isolated from the Sea of Japan. Microbes Environ 2008; 23:209-14. [DOI: 10.1264/jsme2.23.209] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Lyudmila A. Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture
| | - Masataka Uchino
- Laboratory of Food Science and Technology, Department of Applied Biology and Chemistry, Tokyo University of Agriculture
| | | | - Valery V. Mikhailov
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences
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Romanenko LA, Uchino M, Tanaka N, Frolova GM, Slinkina NN, Mikhailov VV. Occurrence and antagonistic potential of Stenotrophomonas strains isolated from deep-sea invertebrates. Arch Microbiol 2007; 189:337-44. [PMID: 18034228 DOI: 10.1007/s00203-007-0324-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Revised: 10/31/2007] [Accepted: 11/02/2007] [Indexed: 11/30/2022]
Abstract
Stenotrophomonas maltophilia is known to be of significance as opportunistic pathogen as well as a source of biocontrol and bioremediation activities. S. maltophilia strains have been isolated from rhizospheres, soil, clinical material, aquatic habitats, but little is known about Stenotrophomonas strains recovered from marine environments. During a survey of the biodiversity of Pseudomonas-like bacteria associated with deep-sea invertebrates six Stenotrophomonas strains were isolated from sponge, sea urchin, and ophiura specimens collected from differing Pacific areas, including the Philippine Sea, the Fiji Sea and the Bering Sea. 16S rRNA gene sequence analysis confirmed an assignment of marine isolates to the genus Stenotrophomonas as it placed four strains into the S. maltophilia CIP 60.77T cluster and two related to the S. rhizophila DSM 14405T. Together with a number of common characteristics typical of S. maltophilia and S. rhizophila marine isolates exhibited differences in pigmentation, a NaCl tolerance, a range of temperatures, which supported their growth, substrate utilization pattern, and antibiotics resistance. Strains displayed hemolytic and remarkable inhibitory activity against a number of fungal cultures and Gram-positive microorganisms, but very weak or none against Candida albicans. This is the first report on isolation, taxonomic characterization and antimicrobial activity of Stenotrophomonas strains isolated from deep-sea invertebrates.
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Affiliation(s)
- Lyudmila A Romanenko
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Prospect 100 Let Vladivostoku, 159, Russia.
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