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Journal Article•DOI•

Marinobacterium maritimum sp. nov., a marine bacterium isolated from Arctic sediment.

So-Jeong Kim1, Soo-Je Park1, Dae-No Yoon1, Byoung-Joon Park1, Boram Choi1, Dong-Hun Lee1, Yul Roh2, Sung-Keun Rhee1 •
Chungbuk National University1, Chonnam National University2
01 Dec 2009-International Journal of Systematic and Evolutionary Microbiology (Microbiology Society)-Vol. 59, Iss: 12, pp 3030-3034
TL;DR: It is proposed that strain AR11(T) (=KCTC 22254(T)=JCM 15134(T)) represents the type strain of a novel species, Marinobacterium maritimum sp.
Abstract: A Gram-negative, aerobic, rod-shaped, motile, marine bacterium, strain AR11T, was isolated from Arctic marine sediment. Strain AR11T grew with 0.5–7 % NaCl and at 7–37 °C and pH 5.5–9.0. It utilized propionate, 3-hydroxybenzoate, l-proline, acetate, d- and l-lactate, l-alanine, malate and phenylacetic acid. Alkaline phosphatase, esterase lipase (C8), leucine arylamidase and acid phosphatase activity tests were positive. Acid was produced from 5-ketogluconate and aesculin. Strain AR11T possessed C16 : 0 (22.0 %), summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 28.1 %) and summed feature 7 (one or more of C18 : 1 ω7c, ω9t and ω12t; 34.0 %) as the major cellular fatty acids. The major ubiquinone was Q-8. Comparative 16S rRNA gene sequence studies showed that strain AR11T belonged to the Gammaproteobacteria and was most closely related to Marinobacterium stanieri DSM 7027T, Marinobacterium halophilum mano11T and Marinobacterium georgiense KW-40T (97.8, 97.0 and 96.7 % similarity, respectively). The G+C content of the genomic DNA of strain AR11T was 57.9 mol%. DNA–DNA relatedness data indicated that strain AR11T represented a distinct species that was separated from M. stanieri DSM 7027T, M. halophilum KCTC 12240T and M. georgiense JCM 21667T. On the basis of evidence from this polyphasic study, it is proposed that strain AR11T (=KCTC 22254T=JCM 15134T) represents the type strain of a novel species, Marinobacterium maritimum sp. nov.
Citations
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Journal Article•DOI•
Dimethylsulphopropionate (DMSP) and proline from the surface of the brown alga Fucus vesiculosus inhibit bacterial attachment

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Mahasweta Saha, Martin Rempt1, Björn Gebser2, Jan Grueneberg1, Georg Pohnert1, Florian Weinberger •
University of Jena1, Max Planck Society2
18 Jun 2012-Biofouling
TL;DR: It is shown that DMSP and proline have an ecologically relevant role as surface inhibitors against bacterial attachment on F. vesiculosus.
Abstract: It was demonstrated previously that polar and non-polar surface extracts of the brown alga Fucus vesiculosus collected during winter from the Kiel Bight (Germany) inhibited bacterial attachment at natural concentrations. The present study describes the bioassay-guided identification of the active metabolites from the polar fraction. Chromatographic separation on a size-exclusion liquid chromatography column and bioassays identified an active fraction that was further investigated using nuclear magnetic resonance spectroscopy and mass spectrometry. This fraction contained the metabolites dimethylsulphopropionate (DMSP), proline and alanine. DMSP and proline caused the anti-attachment activity. The metabolites were further quantified on the algal surface together with its associated boundary layer. DMSP and proline were detected in the range 0.12–1.08 ng cm−2 and 0.09–0.59 ng cm−2, respectively. These metabolites were tested in the concentration range from 0.1 to 1000 ng cm−2 against the attachment of five bacterial strains isolated from algae and sediment co-occurring with F. vesiculosus. The surface concentrations for 50% inhibition of attachment of these strains were always <0.38 ng cm−2 for DMSP and in four cases <0.1 ng cm−2 for proline, while one strain required 1.66 ng cm−2 of proline for 50% inhibition. Two further bacterial strains that had been directly isolated from F. vesiculosus were also tested, but proved to be the least sensitive. This study shows that DMSP and proline have an ecologically relevant role as surface inhibitors against bacterial attachment on F. vesiculosus.

59 citations

Cites background from "Marinobacterium maritimum sp. nov.,..."

  • ...…and S. baltica (isolated from the surfaces of the alga itself) was promoted and weakly inhibited, respectively, when proline was present at natural concentration, corresponding to the fact that several bacteria are known to use free amino acids as a suitable source of carbon (eg Kim et al. 2009)....

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Journal Article•DOI•
Defence Chemistry Modulation by Light and Temperature Shifts and the Resulting Effects on Associated Epibacteria of Fucus vesiculosus

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Mahasweta Saha, Martin Rempt1, Stephanie B. Stratil, Martin Wahl, Georg Pohnert1, Florian Weinberger •
University of Jena1
31 Oct 2014-PLOS ONE
TL;DR: The capacity of F. vesiculosus for antifouling defence chemicals against epibacteria will hardly be compromised by shading or warming to temperatures up to 25°C, it is concluded.
Abstract: The goals of this study were (1) to investigate whether Fucus vesiculosus regulates the production of its antifouling defence chemicals against epibacteria in response to light limitation and temperature shifts and (2) to investigate if different surface concentrations of defence compounds shape epibacterial communities. F. vesiculosus was incubated in indoor mesocosms at five different temperature conditions (5 to 25°C) and in outdoor mesocosms under six differently reduced sunlight conditions (0 to 100%), respectively. Algal surface concentrations of previously identified antifouling compounds - dimethylsulphopropionate (DMSP), fucoxanthin and proline – were determined and the bacterial community composition was characterized by in-depth sequencing of the 16S-rRNA gene. Altogether, the effect of different treatment levels upon defence compound concentrations was limited. Under all conditions DMSP alone appeared to be sufficiently concentrated to warrant for at least a partial inhibitory action against epibiotic bacteria of F. vesiculosus. In contrast, proline and fucoxanthin rarely reached the necessary concentration ranges for self-contained inhibition. Nonetheless, in both experiments along with the direct influence of temperature and light, all three compounds apparently affected the overall bacterial community composition associated with F. vesiculosus since tendencies for insensitivity towards all three compounds were observed among bacterial taxa that typically dominate those communities. Given that the concentrations of at least one of the compounds (in most cases DMSP) were always high enough to inhibit bacterial settlement, we conclude that the capacity of F. vesiculosus for such defence will hardly be compromised by shading or warming to temperatures up to 25°C.

35 citations

Cites background from "Marinobacterium maritimum sp. nov.,..."

  • ...Likewise, various bacteria and other microorganisms have a capacity for uptake and metabolization of proline [28]....

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Journal Article•DOI•
Marinobacterium lutimaris sp. nov., isolated from a tidal flat

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Jeong Myeong Kim1, Se Hee Lee1, Ji Young Jung1, Che Ok Jeon1•
Chung-Ang University1
01 Aug 2010-International Journal of Systematic and Evolutionary Microbiology
TL;DR: A Gram-staining-negative, moderately halophilic bacterium, isolated from a tidal flat of the Taean coast in South Korea, is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacteria lutimaris sp.
Abstract: A Gram-staining-negative, moderately halophilic bacterium, designated strain AN9T, was isolated from a tidal flat of the Taean coast in South Korea. Cells were catalase- and oxidase-positive short rods that were motile by means of a single polar flagellum. Growth of strain AN9T was observed at 15–40 °C (optimum, 25–30 °C) and at pH 6.0–8.0 (optimum, pH 6.5–7.5). Strain AN9T contained ubiquinone Q-8 as the predominant isoprenoid quinone and C10 : 0 3-OH (31.7 %), C18 : 1 ω7c (24.8 %), C16 : 0 (14.7 %) and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH, 10.72 %) as the major fatty acids. The G+C content of the genomic DNA of strain AN9T was 58 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AN9T was related to members of the genus Marinobacterium and was related most closely to Marinobacterium litorale IMCC1877T (96.8 % similarity). On the basis of chemotaxonomic and molecular data, strain AN9T is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium lutimaris sp. nov. is proposed. The type strain is AN9T (=KACC 13703T =DSM 22012T).

33 citations

Cites background or result from "Marinobacterium maritimum sp. nov.,..."

  • ...The genus Marinobacterium, a member of the Gammaproteobacteria, was proposed by González et al. (1997) with the description of Marinobacterium georgiense, and many Marinobacterium species have been isolated from marine sediments (Chang et al., 2007; Kim et al., 2007, 2009a, b; Huo et al., 2009)....

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  • ...The major lipoquinone, major fatty acids and DNA G+C content were in accordance with those of members of the genus Marinobacterium (Chang et al., 2007; Huo et al., 2009; Kim et al., 2007, 2009a, b)....

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Journal Article•DOI•
Dimethylsulfide sources from microalgae: Improvement and application of a derivatization-based method for the determination of dimethylsulfoniopropionate and other zwitterionic osmolytes in phytoplankton

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Astrid Spielmeyer1, Bjoern Gebser2, Georg Pohnert1•
Schiller International University1, Max Planck Society2
20 Mar 2011-Marine Chemistry
TL;DR: In this article, the authors improved and validated a protocol for the derivatization and determination of Dimethylsulfoniopropionate (DMSP) in phytoplankton cultures.

32 citations

Cites background from "Marinobacterium maritimum sp. nov.,..."

  • ...…and S. baltica (isolated from the surfaces of the alga itself) was promoted and weakly inhibited, respectively, when proline was present at natural concentration, corresponding to the fact that several bacteria are known to use free amino acids as a suitable source of carbon (eg Kim et al. 2009)....

    [...]

Journal Article•DOI•
Marinobacterium mangrovicola sp. nov., a marine nitrogen-fixing bacterium isolated from mangrove roots of Rhizophora mangle.

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Gabriela Alfaro-Espinoza1, Matthias S. Ullrich1•
Jacobs University Bremen1
01 Dec 2014-International Journal of Systematic and Evolutionary Microbiology
TL;DR: DNA-DNA relatedness analysis indicated that strain Gal22(T) was different from M. lutimaris DSM 22012(T), and a novel species, Marinobacterium mangrovicola sp.
Abstract: A nitrogen-fixing marine bacterium, designated strain Gal22T, was isolated from mangrove roots of Rhizophora mangle. Cells were Gram-stain-negative rods, motile with a single polar flagellum. Growth was observed at 4–42 °C, pH 5.5 to 10 and with 0–18 % (w/v) NaCl. Strain Gal22T was positive for catalase and oxidase. Q-8 was the predominant lipoquinone. The DNA G+C content was 57.0 mol%. Based on phylogenetic analysis of 16S rRNA gene, strain Gal22T belongs to the genus Marinobacterium . The closely related strains were shown to be Marinobacterium lutimaris DSM 22012T and Marinobacterium litorale IMCC1877T with 99 % and 96 % 16S rRNA gene sequence similarity, respectively. DNA–DNA relatedness analysis indicated that strain Gal22T was different from M. lutimaris DSM 22012T. On the basis of genotypic, morphological and biochemical characteristics, a novel species, Marinobacterium mangrovicola sp. nov. (type strain, Gal22T = DSM 27697T = CIP 110653T), is proposed.

26 citations

Cites background from "Marinobacterium maritimum sp. nov.,..."

  • ...…al., 1983; Bowditch et al., 1984; Satomi et al., 2002), tidal flats of Korea (Chang et al., 2007; Kim et al., 2010), surface water of the Yellow Sea (Kim et al., 2007, 2009a), rhizosphere of a coastal plant (Suaeda japonica) in Korea (Kim et al., 2008), marine sediment of the East China Sea (Huo…...

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  • ...Phenotypic characteristics that differentiate Gal22T from related species of the genus Marinobacterium Strains: 1, Gal22T; 2, M. lutimaris DSM 22012T; 3, M. litorale DSM 23545T; 4, M. marisflavi IMCC4074T (data from Kim et al., 2009a); 5, M. nitratireducens CN44T (data from Huo et al., 2009)....

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  • ...This genus belongs to the class Gammaproteobacteria and at the time of writing comprises 12 species isolated from different marine environments such as a salt marsh on the coast of Georgia (González et al., 1997), sea water of Hawaii (Baumann et al., 1983; Bowditch et al., 1984; Satomi et al., 2002), tidal flats of Korea (Chang et al., 2007; Kim et al., 2010), surface water of the Yellow Sea (Kim et al., 2007, 2009a), rhizosphere of a coastal plant (Suaeda japonica) in Korea (Kim et al., 2008), marine sediment of the East China Sea (Huo et al., 2009), Arctic marine sediment (Kim et al., 2009b) and mucus of a reefbuilder coral from Brazil (Chimetto et al., 2011)....

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  • ...…water of the Yellow Sea (Kim et al., 2007, 2009a), rhizosphere of a coastal plant (Suaeda japonica) in Korea (Kim et al., 2008), marine sediment of the East China Sea (Huo et al., 2009), Arctic marine sediment (Kim et al., 2009b) and mucus of a reefbuilder coral from Brazil (Chimetto et al., 2011)....

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References
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Journal Article•DOI•
The neighbor-joining method: a new method for reconstructing phylogenetic trees.

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Naruya Saitou1, Masatoshi Nei•
University of Texas Health Science Center at Houston1
01 Jul 1987-Molecular Biology and Evolution
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

57,055 citations

"Marinobacterium maritimum sp. nov.,..." refers methods in this paper

  • ...Phylogenetic trees were constructed based on the neighbour-joining (Saitou & Nei, 1987) and maximum-likelihood (Felsenstein, 1981) methods by using the MEGA 3 program (Kumar et al., 2004) and PHYLIP package (Felsenstein, 1993), respectively....

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Journal Article•DOI•
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

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Julie D. Thompson1, Toby J. Gibson, Frederica Plewniak1, Francois Jeanmougin1, Desmond G. Higgins2 •
French Institute of Health and Medical Research1, University College Cork2
01 Dec 1997-Nucleic Acids Research
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Abstract: CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

38,522 citations

"Marinobacterium maritimum sp. nov.,..." refers methods in this paper

  • ...Sequence alignments were performed using the CLUSTAL_X program (Thompson et al., 1997) and gaps were edited in the BioEdit program (Hall, 1999)....

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Journal Article•DOI•
Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/ nt

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Thomas A. Hall
01 Jan 1999-Nucleic Acids Symposium Series

35,309 citations

Journal Article•
PHYLIP-Phylogeny inference package (Version 3.2)

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J. Felsenstein
01 Jan 1989-Cladistics

16,851 citations

Journal Article•DOI•
Evolutionary trees from DNA sequences: A maximum likelihood approach

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Joseph Felsenstein1•
University of Washington1
01 Jan 1981-Journal of Molecular Evolution
TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.
Abstract: The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.

13,111 citations

"Marinobacterium maritimum sp. nov.,..." refers methods in this paper

  • ...Phylogenetic trees were constructed based on the neighbour-joining (Saitou & Nei, 1987) and maximum-likelihood (Felsenstein, 1981) methods by using the MEGA 3 program (Kumar et al., 2004) and PHYLIP package (Felsenstein, 1993), respectively....

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  • ...Phylogenetic trees were constructed based on the neighbour-joining (Saitou & Nei, 1987) and maximum-likelihood (Felsenstein, 1981) methods by using the MEGA 3 program (Kumar et al....

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Related Papers (5)
Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., Two Marine Bacteria from a Lignin-Rich Pulp Mill Waste Enrichment Community

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01 Apr 1997-International Journal of Systematic and Evolutionary Microbiology
José M. González, Frank Mayer, Mary Ann Moran, Robert E. Hodson, William B. Whitman 
Marinobacterium lutimaris sp. nov., isolated from a tidal flat

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01 Aug 2010-International Journal of Systematic and Evolutionary Microbiology
Jeong Myeong Kim, Se Hee Lee, Ji Young Jung, Che Ok Jeon 
Marinobacterium litorale sp. nov. in the order Oceanospirillales.

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01 Jul 2007-International Journal of Systematic and Evolutionary Microbiology
Hana Kim, Yoe-Jin Choo, Jaeho Song, Jung-Sook Lee, Keun Chul Lee, Jang-Cheon Cho 
Marinobacterium nitratireducens sp. nov. and Marinobacterium sediminicola sp. nov., isolated from marine sediment.

[...]

01 May 2009-International Journal of Systematic and Evolutionary Microbiology
Ying-Yi Huo, Xue-Wei Xu, Yi Cao, Chun-Sheng Wang, Xu-Fen Zhu, Aharon Oren, Min Wu 
Marinobacterium rhizophilum sp. nov., isolated from the rhizosphere of the coastal tidal-flat plant Suaeda japonica.

[...]

01 Jan 2008-International Journal of Systematic and Evolutionary Microbiology
Yoon-Gon Kim, Yeon-A Jin, Chung Yeon Hwang, Byung Cheol Cho