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Journal ArticleDOI

Marinobacterium coralli sp. nov., isolated from mucus of coral (Mussismilia hispida)

TL;DR: DNA-DNA hybridizations between strain R-40509(T) and the type strains of the phylogenetically closest species of the genus Marinobacterium revealed less than 70 % DNA-DNA relatedness, supporting the novel species status of the strain.
Abstract: A Gram-negative, aerobic bacterium, designated R-40509T, was isolated from mucus of the reef builder coral (Mussismilia hispida) located in the Sao Sebastiao Channel, Sao Paulo, Brazil. The strain was oxidase-positive and catalase-negative, and required Na+ for growth. Its phylogenetic position was in the genus Marinobacterium and the closest related species were Marinobacterium sediminicola, Marinobacterium maritimum and Marinobacterium stanieri; the isolate exhibited 16S rRNA gene sequence similarities of 97.5–98.0 % with the type strains of these species. 16S rRNA gene sequence similarities with other type strains of the genus Marinobacterium were below 96 %. DNA–DNA hybridizations between strain R-40509T and the type strains of the phylogenetically closest species of the genus Marinobacterium revealed less than 70 % DNA–DNA relatedness, supporting the novel species status of the strain. Phenotypic characterization revealed that the strain was able to grow at 15–42 °C and in medium containing up to 9 % NaCl. The isolate could be differentiated from phenotypically related species by several features, including its ability to utilize d-alanine, l-alanine, bromosuccinic acid, β-hydroxybutyric acid and α-ketovaleric acid, but not acetate or l-arabinose. It produced acetoin (Voges–Proskauer), but did not have esterase lipase (C8) or catalase activities. It possessed C18 : 1 ω7c (35 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 25 %) and C16 : 0 (22 %) as major cellular fatty acids. The DNA G+C content was 58.5 mol%. The name Marinobacterium coralli sp. nov. is proposed to accommodate this novel isolate; the type strain is R-40509T (=LMG 25435T =CAIM 1449T).
Citations
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Journal ArticleDOI
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 coralli sp. nov., i..."

  • ..., 2009b) and mucus of a reefbuilder coral from Brazil (Chimetto et al., 2011)....

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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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Book ChapterDOI
01 Jan 2012
TL;DR: The aim of this chapter was to establish an overview on the microbial diversity studies carried out in Brazil mainly in the last 5 years, including taxonomic studies based on cultured microorganisms and culture-independent studiesbased on molecular fingerprints and 16S rRNA clone libraries, which focuses mainly on prokaryotes with environmental and agricultural importance.
Abstract: Brazil is a megabiodiverse country with approximately 20% of the total number of described species on the planet (Mittermeier et al. 2004). It has the largest tropical forest cover (>6 million km2, corresponding to approximately 30 times the area of the United Kingdom or approx. 20 times the area of Germany) and one of the largest marine realms (>4 million km2) of the planet. The diversity of biomes (e.g., the Amazon and Atlantic Forests, Southern Plains or Pampas, Cerrado (a savanna-like vegetation), Pantanal (wetlands), Caatinga, coral reefs, oceanic islands, mangroves, salt marshes, coastal environments, and deep sea; (IBGE 2004)) allows for the diversification of a variety of life forms. Between 1999 and 2009, more than 1,200 new species of plants and vertebrates were discovered only in the Amazon region, corresponding to one new discovery every 3 days (WWF 2010). There is indeed a considerable amount of literature on the biodiversity of plants and animals in Brazil. Their diversity is used as a basic parameter in the implementation of management actions on priority areas for conservation and protection (Myers et al. 2000). Studies on the microbial diversity are comparatively much scarcer. For instance, only recently the microbial diversity of Amazon and Cerrado soils and the marine realm have been studied in a systematic way. The aim of this chapter was to establish an overview on the microbial diversity studies (N = 150) carried out in Brazil mainly in the last 5 years, including taxonomic studies based on cultured microorganisms and culture-independent studies based on molecular fingerprints and 16S rRNA clone libraries. The chapter focuses mainly on prokaryotes with environmental (e.g., coral holobionts), agricultural (e.g., crop promoting), and biotechnological importance (e.g., bioremediation).

17 citations

Journal ArticleDOI
TL;DR: Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain DB-1T is separated from recognized species of the genus Marinobacterium.
Abstract: A Gram-stain-negative, motile, aerobic, rod- or ovoid-shaped bacterium, designated DB-1T, was isolated from a tidal flat on the Yellow Sea in South Korea and subjected to a taxonomic study using a polyphasic approach. Strain DB-1T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 0.5–2.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain DB-1T falls within the clade comprising species of the genus Marinobacterium, clustering coherently with the type strain of Marinobacterium nitratireducens and showing a sequence similarity value of 98.4 %. The novel strain exhibited 16S rRNA gene sequence similarities of 91.5–94.4 % to the type strains of other species of the genus Marinobacterium. Strain DB-1T contained Q-8 as the predominant ubiquinone and C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids detected in strain DB-1T were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid, one unidentified glycolipid, one unidentified phospholipid and two unidentified lipids. The DNA G+C content of strain DB-1T was 62.3 mol% and the mean DNA–DNA relatedness value with the type strain of M. nitratireducens was 21 ± 4.6 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain DB-1T is separated from recognized species of the genus Marinobacterium. On the basis of the data presented, strain DB-1T is considered to represent a novel species of the genus Marinobacterium, for which the name Marinobacterium aestuariivivens sp. nov. is proposed. The type strain is DB-1T ( = KCTC 42778T = NBRC 111756T).

16 citations


Cites background from "Marinobacterium coralli sp. nov., i..."

  • ...Members of the genus Marinobacterium have been isolated from a variety of marine environments, marine organisms and mangrove roots (Baumann et al., 1972; González et al., 1997; Chang et al., 2007; Kim et al., 2007, 2010; Huo et al., 2009; Chimetto et al., 2011; Alfaro-Espinoza & Ullrich, 2014)....

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  • ...Members of the genus Marinobacterium have been isolated from a variety of marine environments, marine organisms and mangrove roots (Baumann et al., 1972; González et al., 1997; Chang et al., 2007; Kim et al., 2007, 2010; Huo et al., 2009; Chimetto et al., 2011; Alfaro-Espinoza & Ullrich, 2014)....

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Journal ArticleDOI
TL;DR: Based on the phylogenetic, chemotaxonomic, genomic and phenotypic data presented, a novel species with the name Marinobacterium profundum sp.
Abstract: A Gram-stain-negative, rod-shaped and motile strain, designated PAMC 27536T, was isolated from deep-sea sediment in the East Sea, Korea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Marinobacterium. Phylogenetic analyses revealed that strain PAMC 27536T was related most closely to Marinobacterium rhizophilum CL-YJ9T with a 16S rRNA gene sequence similarity of 98.5 % and to other members of the genus Marinobacterium (94.0–91.7 %). Genomic relatedness analyses between strain PAMC 27536T and M. rhizophilum KCCM 42386T gave an average nucleotide identity of 85.6 % and an estimated DNA–DNA hybridization of 24.6 % using the genome-to-genome distance calculator, indicating that they represent genomically distinct species. Cells of strain PAMC 27536T grew optimally at 25–30 °C and pH 7.0–7.5 in the presence of 3 % (w/v) sea salts. The major cellular fatty acids were C16 : 1ω6c and/or C16 : 1ω7c, C18 : 1ω6c and/or C18 : 1ω7c, and C16 : 0. The major isoprenoid quinone was Q-8. The genomic DNA G+C content was 56.1–57.2 mol%. Based on the phylogenetic, chemotaxonomic, genomic and phenotypic data presented, a novel species with the name Marinobacterium profundum sp. nov. is proposed, with PAMC 27536T ( = KCCM 43095T = JCM 30410T) as the type strain.

13 citations


Cites background from "Marinobacterium coralli sp. nov., i..."

  • ...…: 1v7c (42.7 %), C18 : 1v6c and/or C18 : 1v7c (20.9 %), and C16 : 0 (19.1 %; Table S1, available in the online Supplementary Material), which are typically found as major components in members of the genus Marinobacterium (Kim et al., 2008; Chimetto et al., 2011; Alfaro-Espinoza & Ullrich, 2014)....

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  • ...1 %; Table S1, available in the online Supplementary Material), which are typically found as major components in members of the genus Marinobacterium (Kim et al., 2008; Chimetto et al., 2011; Alfaro-Espinoza & Ullrich, 2014)....

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  • ...The genus Marinobacterium belongs to the family Alteromonadaceae, and members of this genus contain C16 : 1v6c and/or C16 : 1v7c, C18 : 1v6c and/or C18 : 1v7c, and C16 : 0 as the major fatty acids and Q-8 as the major respiratory quinone (González et al., 1997; Kim et al., 2008; Chimetto et al., 2011; Alfaro-Espinoza & Ullrich, 2014)....

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  • ...…family Alteromonadaceae, and members of this genus contain C16 : 1v6c and/or C16 : 1v7c, C18 : 1v6c and/or C18 : 1v7c, and C16 : 0 as the major fatty acids and Q-8 as the major respiratory quinone (González et al., 1997; Kim et al., 2008; Chimetto et al., 2011; Alfaro-Espinoza & Ullrich, 2014)....

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  • ...…M. lutimaris, Kim et al., 2010), roots of salt-tolerant plants (M. rhizophilum, Kim et al., 2008; M.mangrovicola, Alfaro-Espinoza&Ullrich, 2014), sediments (M. nitratireducens and M. sediminicola, Huo et al., 2009; M. maritimum, Kim et al., 2009b) and coral (M. coralli, Chimetto et al., 2011)....

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Journal ArticleDOI
TL;DR: Based on the phylogenetic, physiological and biochemical characteristics, strain HS6T represents a novel genus and species and the name Motiliproteus sediminis gen. nov., sp.
Abstract: A novel Gram-stain-negative, rod-to-spiral-shaped, oxidase- and catalase- positive and facultatively aerobic bacterium, designated HS6T, was isolated from marine sediment of Yellow Sea, China. It can reduce nitrate to nitrite and grow well in marine broth 2216 (MB, Hope Biol-Technology Co., Ltd) with an optimal temperature for growth of 30–33 °C (range 12–45 °C) and in the presence of 2–3 % (w/v) NaCl (range 0.5–7 %, w/v). The pH range for growth was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel isolate was 93.3 % similar to the type strain of Neptunomonas antarctica, 93.2 % to Neptunomonas japonicum and 93.1 % to Marinobacterium rhizophilum, the closest cultivated relatives. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol and some other unknown lipids. Major cellular fatty acids were summed feature 3 (C16:1 ω7c/iso-C15:0 2-OH), C18:1 ω7c and C16:0 and the main respiratory quinone was Q-8. The DNA G+C content of strain HS6T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical characteristics, strain HS6T represents a novel genus and species and the name Motiliproteus sediminis gen. nov., sp. nov., is proposed. The type strain is HS6T (=ATCC BAA-2613T=CICC 10858T).

13 citations


Cites background from "Marinobacterium coralli sp. nov., i..."

  • ...…1983; González et al. 1997; Chang et al. 2007; Kim et al. 2007; Kim et al. 2008; Huo et al. 2009; Kim et al. 2009a; Kim et al. 2009b; Kim et al. 2010; Chimetto et al. 2011); Neptuniibacter (Arahal et al. 2007; Chen et al. 2012); Nitrincola (Dimitriu et al. 2005) ? positive, - negative, F…...

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  • ...2013); Marinobacterium (Baumann et al. 1983; González et al. 1997; Chang et al. 2007; Kim et al. 2007; Kim et al. 2008; Huo et al. 2009; Kim et al. 2009a; Kim et al. 2009b; Kim et al. 2010; Chimetto et al. 2011); Neptuniibacter (Arahal et al....

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References
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Journal ArticleDOI
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


Additional excerpts

  • ...Trees were drawn using the neighbour-joining (Saitou & Nei, 1987), maximum-parsimony (Eck & Dayhoff, 1966) and minimum evolution methods (Rzhetsky & Nei, 1992)....

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Journal ArticleDOI
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Abstract: The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.

40,349 citations


"Marinobacterium coralli sp. nov., i..." refers methods in this paper

  • ...The robustness of the tree topologies was checked by 1000 bootstrap replications (Felsenstein, 1985)....

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Journal ArticleDOI
TL;DR: Version 4 of MEGA software expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses.
Abstract: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).

29,021 citations


Additional excerpts

  • ...0 (Tamura et al., 2007) and BioNumerics 4.5....

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Journal ArticleDOI
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Abstract: Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or “transition” type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or “transversion” type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = — (1/2) ln {(1 — 2P — Q) }. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = — (1/2) ln (1 — 2P — Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.

26,016 citations


"Marinobacterium coralli sp. nov., i..." refers methods in this paper

  • ...Evolutionary distances were computed using the Kimura 2-parameter method (Kimura, 1980)....

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Book
01 Jan 1965

6,855 citations


Additional excerpts

  • ...Trees were drawn using the neighbour-joining (Saitou & Nei, 1987), maximum-parsimony (Eck & Dayhoff, 1966) and minimum evolution methods (Rzhetsky & Nei, 1992)....

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