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At least 19 recordsLinked to original sources

PubMed2004

Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov.

The phylogenetic relationships among marine Alteromonas-like bacteria of the genera Alteromonas, Pseudoalteromonas, Glaciecola, Thalassomonas, Colwellia, Idiomarina, Oceanimonas, Oceanisphaera, Shewanella, Moritella, Ferrimonas, Psychromonas and several other genera of the 'Gammaproteobacteria' were studied. Results of 16S rRNA gene sequence analyses revealed that some members of these genera formed several coherent groups at the family level. Characteristic signature oligonucleotides for studied taxa were defined. Signature positions are divided into three classes: (i) single compensatory mutations, (ii) double compensatory mutations and (iii) mutations affecting nucleotides not paired in the secondary structure. The 16S rRNA gene sequence similarity level within genera was 93 % or above. This value can be a useful additional criterion for genus discrimination. On the basis of this work and previous polyphasic taxonomic studies, the circumscription of the family Alteromonadaceae is limited to the genera Alteromonas and Glaciecola and the creation is proposed of the families Pseudoalteromonadaceae fam. nov. to accommodate bacteria of the genera Pseudoalteromonas and Algicola gen. nov. (formerly Pseudoalteromonas bacteriolytica) and Colwelliaceae fam. nov. to accommodate bacteria of the genera Colwellia and Thalassomonas. Bacteria of the genera Oceanimonas and Oceanisphaera formed a robust cluster and shared common signature oligonucleotides. Because of deep branching and lack of association with any other genus, the following families are proposed that include single genera: Idiomarinaceae fam. nov., Psychromonadaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov. and Shewanellaceae fam. nov. Finally, this study also revealed that [Hyphomicrobium] indicum should be reclassified as Photobacterium indicum comb. nov.

Alteromonas↗

PubMedDate not supplied

[A new family of Alteromonadaceae fam. nov., including the marine proteobacteria species Alteromonas, Pseudoalteromonas, Idiomarina i Colwellia].

The taxonomic position of the marine genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia within the gamma subclass of the class Proteobacteria were specified on the basis of their phenotypic, genotypic, and phylogenetic characteristics. Gram-negative aerobic bacteria of the genera Alteromonas, Pseudoalteromonas, and Idiomarina and facultatively anaerobic bacteria of the genus Colwellia were found to form a phylogenetic cluster with a 16S rRNA sequence homology of 90% or higher. The characteristics of these genera presented in this paper allow their reliable taxonomic identification. Based on the analysis of our experimental data and analyses available in the literature, we propose to combine the genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia into a new family, Alteromonadaceae fam. nov., with the type genus Alteromonas.

Alteromonas↗

PubMed2005

Salinimonas chungwhensis gen. nov., sp. nov., a moderately halophilic bacterium from a solar saltern in Korea.

A halophilic non-spore-forming bacterium of the gamma-Proteobacteria, designated strain BH030046T, was isolated from a solar saltern in Korea. Cells were Gram-negative, chemoheterotrophic, short rod-shaped and motile with a polar flagellum. Comparative 16S rRNA gene sequence analysis revealed that strain BH030046T formed a distinct lineage in the family Alteromonadaceae and was distinguished from its closest related genera Alteromonas (91.4-94.8 %), Aestuariibacter (92.1-93.5 %) and Glaciecola (92.1-93.5 %) on the basis of low 16S rRNA gene sequence similarities. Physiological and biochemical data also showed that the isolate was different from members of these three genera. The predominant cellular fatty acids were C(16 : 0) and C(18 : 1)omega7c. DNA G+C content was 48 mol% and the major isoprenoid quinone was Q-8. The strain grew optimally at 30-35 degrees C, pH 7.0-8.0 and 2-5 % NaCl. On the basis of physiological and molecular properties, strain BH030046T (=KCTC 12239T=DSM 16280T) represents a novel genus and species in the family Alteromonadaceae, for which the name Salinimonas chungwhensis gen. nov., sp. nov. is proposed.

Alteromonadaceae↗

PubMed2004

Isolation and characterization of a fucoidan-degrading marine bacterial strain and its fucoidanase.

A marine bacterial strain that degraded fucoidan from Kjellmaniella crassifolia (class Phaeophyceae, order Laminariales, family Laminariaceae) was isolated in our laboratory. The strain was gram-negative, ubiquinone 8 was the predominant respiratory quinone, and the GC-content of its genomic DNA was 36%. The cells of the strain were rod-shaped (2.0 microm long x 1.0 microm wide), and each cell was motile by means of one polar flagellum. Phylogenetic analysis of its 16S ribosomal DNA sequence indicated that it was a member of the family Alteromonadaceae. It produced a type of extracellular fucoidanase, an endosulfated fucan-digesting enzyme. The enzyme was purified with 3500-fold purity at 12.0% yield. Optimum conditions for the enzyme reaction were approximately pH 6.5 to 8.0 and temperature 30 degrees to 35 degrees C. The enzyme was activated by calcium ions, and maximum activity was observed in the presence of greater than 30 mM calcium ion.

Alteromonadaceae↗

PubMed2004

Aestuariibacter salexigens gen. nov., sp. nov. and Aestuariibacter halophilus sp. nov., isolated from tidal flat sediment, and emended description of Alteromonas macleodii.

Two strictly aerobic, halophilic strains of the gamma-Proteobacteria, designated JC2042(T) and JC2043(T), were obtained from a sediment sample of getbol, the Korean tidal flat. Comparative 16S rDNA sequence studies revealed that the test strains were related most closely to the type strains of the genera Alteromonas (93.5-95.5 %) and Glaciecola (91.1-93.3 %). Phylogenetic analyses demonstrated that strains JC2042(T) and JC2043(T) formed a distinct monophyletic clade within the family Alteromonadaceae and clustered distantly with the genera Alteromonas and Glaciecola. Physiological, biochemical and chemotaxonomic data also indicated that the two getbol isolates were significantly different from members of these two genera and others with validly published names. Cells were rod-shaped and motile with a polar flagellum. The major isoprenoid quinone was Q8. The predominant cellular fatty acids were C(16 : 0), C(18 : 1)omega7c and a mixture of C(16 : 1)omega7c and iso-C(15 : 0) 2-OH. DNA G+C contents were 48-54 mol%. On the basis of this polyphasic study, Aestuariibacter gen. nov. is proposed with two novel species, Aestuariibacter salexigens sp. nov. (type strain, JC2042(T)=IMSNU 14006(T)=KCTC 12042(T)=DSM 15300(T)) and Aestuariibacter halophilus sp. nov. (type strain, JC2043(T)=IMSNU 14007(T)=KCTC 12043(T)=DSM 15266(T)). Aestuariibacter salexigens is the type species of the genus. In addition, an emended description of Alteromonas macleodii is proposed.

Acetylglucosamine↗

PubMed2003

Structures of polysaccharides and oligosaccharides of some Gram-negative marine Proteobacteria.

The chemical structures of polysaccharides and LPS core oligosaccharides, isolated from various Gram-negative marine bacteria from the genera Pseudoalteromonas and Shewanella belonging to the Alteromonadaceae family and gamma-subclass of Proteobacteria, are reviewed. The polysaccharides are distinguished by the acidic character (e.g., due to the presence of hexuronic and aldulosonic acids and their derivatives) and the occurrence of unusual sugars, including N-acyl derivatives of 6-deoxyamino sugars, such as N-acetyl-D-quinovosamine, N-acetyl-L-fucosamine and N-acetyl-6-deoxy-L-talosamine, and higher sugars like 2,6-dideoxy-2-acetamido-4-C-(3'-carboxamide-2',2'-dihydroxypropyl)-D-galactopyranose (shewanellose). Many constituent sugars have various uncommon non-sugar substituents, such as alanine, formic, lactic and hydroxybutyric acids, sulfate, phosphate, and 2-aminopropane-1,3-diol.

Carbohydrate Conformation↗

PubMed2001

Chemical characterization of lipid A from some marine proteobacteria.

Lipids A from type and wild strains of marine Proteobacteria belonging to Alteromonadaceae (Alteromonas (1 species), Idiomarina (1 species), and Pseudoalteromonas (8 species) genera) and Vibrionaceae (Shewanella (1 species) and Vibrio (1 species) genera) families and Marinomonas genus (1 species) were isolated by hydrolysis of their respective lipopolysaccharides with 1% acetic acid. Based on thin-layer chromatography data, the lipids A studied had low heterogeneity and generated family-specific patterns varying in numbers of bands and their chromatographic mobility. Total chemical analysis of the compounds showed that they contained glucosamine, phosphate, and fatty acids with decanoate (I. zobellii KMM 231(T) lipid A) or dodecanoate (lipids A of the other bacteria) and 3-hydroxy alkanoates as the major fatty acid components. Unlike terrestrial bacterial lipids A, lipids A of marine Proteobacteria had basically monophosphoryl (except V. fluvialis AQ 0002B lipid A with its two phosphate groups) and pentaacyl (except S. alga 48055 and V. fluvialis AQ 0002B lipids A which were found to have six residues of fatty acids per molecule of glucosamine disaccharide) structural types, low toxicity, and may be useful as potential endotoxin antagonists.

Animals↗

PubMed2002

Stimulation of Alexandrium fundyense growth by bacterial assemblages from the Bay of Fundy.

AIMS: To evaluate the influence of marine bacterial assemblages from the Bay of Fundy on Alexandrium fundyense str. CB301 growth. METHODS AND RESULTS: Bacterial assemblages were collected from the Bay of Fundy during an Alexandrium spp. bloom, serially diluted to extinction and inoculated into axenic CB301 cultures. Bacterial assemblages dramatically enhanced CB301 growth. Retrieval and analysis of 16S rDNA fragments revealed an Alteromonas sp. strain to be the only detectable bacterium in all assemblages that promoted A. fundyense and the sole bacterium found in the most dilute inoculum that promoted A. fundyense. While this bacterium has not yet been isolated, other isolates obtained from the assemblages did not stimulate A. fundyense, indicating that the observed stimulation was not a general effect of marine bacteria. CONCLUSIONS: Bay of Fundy marine bacterial assemblages dominated by a member of the family Alteromonadaceae were found to dramatically stimulate growth of A. fundyense. SIGNIFICANCE AND IMPACT OF THE STUDY: These results show that native bacteria have the potential to dramatically promote the growth of A. fundyense and may play an important role in influencing A. fundyense dynamics in the Bay of Fundy.

Alteromonas↗

PubMed2003

Conservation of the response regulator gene gacA in Pseudomonas species.

The response regulator gene gacA influences the production of several secondary metabolites in both pathogenic and beneficial Pseudomonas spp. In this study, we developed primers and a probe for the gacA gene of Pseudomonas species and sequenced a 425 bp fragment of gacA from ten Pseudomonas strains isolated from different plant-associated environments. Polymerase chain reaction analysis and Southern hybridization showed that gacA is highly conserved within the genus Pseudomonas: multiple strains of different Pseudomonas species all responded positively to the probe, whereas no response was obtained from 18 other strains representing 14 species that belong to eight different genera of Gram-negative bacteria other than Pseudomonas. Furthermore, from a total of approximately 550 indigenous bacterial isolates obtained from the rhizosphere of wheat, all isolates that hybridized with the gacA probe were classified as Pseudomonas spp. by group-specific primers. Isolates that did not respond with the gacA probe and primers were identified as bacterial genera other than Pseudomonas, including Stenotrophomonas, Cryseomonas and Comamonas spp. These results indicate that gacA can be used as a complementary genetic marker for detection of Pseudomonas spp. in environmental samples. Phylogenetic relationships inferred from the newly sequenced gacA fragments and the sequences of gacA homologues present in the databases, showed six distinct clusters that correspond to the following bacterial families: Pseudomonaceae, Enterobacteriaceae, Alteromonadaceae, Vibrionaceae, Burkholderia and Xanthomonas. Within the Pseudomonadaceae and Enterobacteriaceae, polymorphisms within gacA and its homologues allowed identification of six and five subclusters respectively. Comparison of the gacA gene and GacA protein-based trees with the tree inferred from 16S rDNA sequences yielded a similar overall clustering. These results suggest that gacA and its homologues may provide complementary markers for phylogenetic studies of Pseudomonas spp. and Gram-negative bacteria other than Pseudomonas.

Bacterial Proteins↗

PubMed2000

Selected chitinase genes in cultured and uncultured marine bacteria in the alpha- and gamma-subclasses of the proteobacteria.

PCR primers were patterned after chitinase genes in four gamma-proteobacteria in the families Alteromonadaceae and Enterobacteriaceae (group I chitinases) and used to explore the occurrence and diversity of these chitinase genes in cultured and uncultured marine bacteria. The PCR results from 104 bacterial strains indicated that this type of chitinase gene occurs in two major groups of marine bacteria, alpha- and gamma-proteobacteria, but not the Cytophaga-Flavobacter group. Group I chitinase genes also occur in some viruses infecting arthropods. Phylogenetic analysis indicated that similar group I chitinase genes occur in taxonomically related bacteria. However, the overall phylogeny of chitinase genes did not correspond to the phylogeny of 16S rRNA genes, possibly due to lateral transfer of chitinase genes between groups of bacteria, but other mechanisms, such as gene duplication, cannot be ruled out. Clone libraries of chitinase gene fragments amplified from coastal Pacific Ocean and estuarine Delaware Bay bacterioplankton revealed similarities and differences between cultured and uncultured bacteria. We had hypothesized that cultured and uncultured chitin-degrading bacteria would be very different, but in fact, clones having nucleotide sequences identical to those of chitinase genes of cultured alpha-proteobacteria dominated both libraries. The other clones were similar but not identical to genes in cultured gamma-proteobacteria, including vibrios and alteromonads. Our results suggest that a closer examination of chitin degradation by alpha-proteobacteria will lead to a better understanding of chitin degradation in the ocean.

Alphaproteobacteria↗

PubMed2026

Microbial membrane transporters reveal trace metal niche adaptation in distinct water masses of the Southern Ocean.

BACKGROUND: Trace metals are co-factors for enzymes that are essential for microbial metabolism and the cycling of major elements. Membrane transporters allow microbes to sense and react to trace elements in the environment and to balance their uptake and export for the regulation of intracellular metal homeostasis. The acquisition and efflux of trace metals could lead to reciprocal feedbacks between microbes and the surrounding environment. Whether these processes vary among trace metals and across habitats is presently not known. We used membrane transporters into and out of the cell as indicators for the uptake and efflux of trace metals and provide a detailed picture of the distribution of the respective genes in distinct provinces in surface waters and in subsurface water masses across a transect in the Southern Indian Ocean. RESULTS: We observed marked spatial and vertical patterns in normalized gene abundances of transporters of iron (Fe), manganese (Mn), nickel (Ni) and copper (Cu). Changes in gene abundances were specific to the type of transporter and trace metal, and pronounced differences between surface and specific water masses emerged. We found an enrichment in genes related to efflux and homeostasis of Fe, Ni and Cu in two water masses of the deep ocean that are North Atlantic Deep Water (NADW) and Lower Circumpolar Deep Water (LCDW). This pattern was observed on the community level and for metagenome-assembled genomes (MAGs) affiliated with Alteromonadaceae and Burkholderiaceae that were abundant in these two water masses. CONCLUSIONS: The enrichment in trace metal efflux and resistance genes points to microbially mediated processes, exerted by homeostasis, with potential influence on the trace metal speciation and distribution in specific water masses in the deep ocean. The gene repertoire and distinct distribution pattern of the taxa identified as potential key players could reflect an adaptation to these old water masses with trace metals acting as selective driver. Video Abstract.

Membrane Transport Proteins↗

PubMed2001

Regulation of aromatic amino acid biosynthesis in gamma-proteobacteria.

Computational comparative techniques were applied to analysis of the aromatic amino acid regulons in gamma-proteobacteria. This resulted in characterization of the TrpR and TyrR regulons in the genomes of Yersinia pestis, Haemophilus influenzae, Vibrio cholerae and other bacteria and identification of new members of the PhhR regulon in the genome of Pseudomonas aeruginosa. Candidate attenuators were constructed for all studied genomes, including the trpBA operon of the very distantly related bacterium Chlamidia trachomatis. The pheA attenuator of Y. pestis is an integration site for the insertion element IS-200. It was shown that the triplication of the DAHP-synthase genes occurred prior to the divergence of families Enterobacteriaceae, Vibrionaceae and Alteromonadaceae. The candidate allosteric control site of the DAHP-syntheases was identified. This site is deteriorated in AroH of Buchnera sp. APS. The known DAHP-synthase of Bordetella pertussis is likely to be feedback-inhibited by phenylalanine, and the DAHP-synthase of Corynebacterium glutamicum could be inhibited by tyrosine. Overall, the most extensive regulation was observed in Escherichia coli, whereas the regulation in other genomes seems to be less developed. At the extreme, the tryptophan production in the aphid endosymbiont Buchnera sp. APS is free from transcriptional, attenuation, and allosteric control.

Allosteric Regulation↗

PubMed2005

The diversity of culturable organotrophic bacteria from local solar salterns.

We isolated and cultured bacteria inhabiting solar saltern ponds in Taean-Gun, Chungnam Province, Korea. All of the isolated 64 strains were found to be moderately halophilic bacteria, growing in a salt range of 2-20 %, with an optimal concentration of 5% salt. Bacterial diversity among the isolated halophiles was evaluated via RFLP analyses of PCR-amplified 16S rDNAs, followed by phylogenetic analysis of the partial 16S rDNA sequences. The combination of restriction enzyme digestions with HaeIII, CfoI, MspI and RsaI generated 54 distinct patterns. A neighbor-joining tree of the partial 16S rDNA sequences resulted in the division of the 64 strains into 2 major groups, 45 strains of gamma-Proteobacteria (70.3%) and 19 strains of Firmicutes (29.7%). The alpha-Proteobacteria and Cytophaga-Flavobacterium-Bacterioides groups, which were repeatedly found to exist in thalassohaline environments, were not represented in our isolates. The gamma-Proteobacteria group consisted of several subgroups of the Vibrionaceae (37.5%), Pseudoalteromonadaceae (10.9%), Halomonadaceae (7.8%), Alteromonadaceae (7.8%), and Idiomarinaceae (6.3%). Members of Salinivibrio costicola (29.7%) were the most predominant species among all of the isolates, followed by Halobacillus treperi (12.5%). Additionally, three new species candidates were found, based on similarities of the 16S rDNA sequences to those of previously published species.

Bacillaceae↗

PubMed2005

Characterization of a novel microperoxidase from Marinobacter hydrocarbonoclasticus by electrospray ionization tandem mass spectrometry.

Microperoxidases are small heme-peptides obtained by proteolytic digestion of cytochrome c, exhibiting peroxidase activity. They consist of a short- or medium-length polypeptide chain, covalently linked to an iron protoporphyrin IX moiety via two thioether bonds involving Cys residues at the c-porphyrin A and B pyrrole rings. These small molecules are interesting for a wide range of possible applications. We have structurally characterized, by means of electrospray ionization (ESI) mass and tandem mass spectrometric experiments, a novel microperoxidase called MMP-5 (Marinobacter MicroPeroxidase-5), obtained by proteolytic digestion of cytochrome c552, a monoheminic electron-transfer protein isolated from Marinobacter hydrocarbonoclasticus. This microperoxidase, which still maintains the functional peptide moieties for peroxidase activity, is devoid of the two amino acids intercalating the Cys residues linked to the c-porphyrin, thus increasing its water solubility. Once submitted to the ESI source potential, MMP-5 showed an interesting tendency for the reduction of the iron protoporphyrin substructure. This behaviour was clearly evidenced by the mass shift exhibited by the reduced form.

Alteromonadaceae↗

PubMed2005

Use of electrospray ionization mass spectrometry for profiling of crude oil effects on the phospholipid molecular species of two marine bacteria.

We investigated the membrane lipid composition of two hydrocarbon-degrading gram-negative bacterial strains (Pseudomonas nautica IP 617 and Marinobacter hydrocarbonoclasticus) initially cultured on a soluble substrate, then on petroleum hydrocarbons, and finally taken back onto the soluble substrate. For the two strains, the growth on petroleum and the return to the initial medium showed major, but comparable, qualitative and quantitative modifications of the intact phospholipid molecular species (IPMS) composition. Furthermore, since bacterial membranes are mainly made up of phospholipids, these modifications reflected hydrocarbon assimilation, restoration abilities and membrane fluidity adaptation. The electrospray ionization mass spectrometry (ESI-MS) analysis of intact phospholipid provided some new information (e.g. sn fatty acyl chain distribution) that could not be assessed by the classical fatty acid analysis. Moreover, such information should be particularly helpful with regards to bacterial taxonomy and xenobiotic toxicity studies.

Alteromonadaceae↗

PubMed2003

Gene structure and transcriptional regulation specific to the groESL operon from the psychrophilic bacterium Colwellia maris.

The groESL operon of a psychrophilic bacterium, Colwellia maris, was cloned and sequenced. The operon contains two ORFs of 291 bp and 1,650 bp separated by 210 bp. Northern blot analysis suggested that the groESL operon was transcribed as a bicistronic mRNA, and that the amount of mRNA markedly increased after the temperature was raised from 10 degrees C to 20 degrees C. Although the optimum temperatures for GroESL function are different in psychrophilic, mesophilic, and thermophilic bacteria, the deduced amino acid sequences of C. maris GroES and GroEL showed remarkably high similarity with those of GroES and GroEL from mesophilic and thermophilic bacteria. A putative promoter similar to the Escherichia coli sigma(32) consensus sequence was identified. One specific feature of C. maris groESL was that in the putative untranslated region the G+C content was about 24 mol%, which is much lower than that of mesophilic bacteria such as E. coli. The low G+C content may be important for maintaining transcription at low temperatures.

Alteromonadaceae↗

PubMed2004

Enzymatic properties and nucleotide and amino acid sequences of a thermostable beta-agarase from a novel species of deep-sea Microbulbifer.

An agar-degrading bacterium, strain JAMB-A7, was isolated from the sediment in Sagami Bay, Japan, at a depth of 1,174 m and identified as a novel species of the genus Microbulbifer. The gene for a novel beta-agarase from the isolate was cloned and sequenced. It encodes a protein of 441 amino acids with a calculated molecular mass of 48,989 Da. The deduced amino acid sequence showed similarity to those of known beta-agarases in glycoside hydrolase family 16, with only 34-55% identity. A sequence similar to a carbohydrate-binding module was found in the C-terminal region of the enzyme. The recombinant agarase was hyper-produced extracellularly using Bacillus subtilis as the host, and the enzyme purified to homogeneity had a specific activity of 398 U (mg protein)(-1) at pH 7.0 and 50 degrees C. It was thermostable, with a half-life of 502 min at 50 degrees C. The optimal pH and temperature for activity were around 7 and 50 degrees C, respectively. The pattern of agarose hydrolysis showed that the enzyme was an endo-type beta-agarase, and the final main product was neoagarotetraose. The activity was not inhibited by NaCl, EDTA, and various surfactants at high concentrations. In particular, sodium dodecyl sulfate had no inhibitory effect up to 2%.

Alteromonadaceae↗

PubMed2004

Cloning, expression, and characterization of a glycoside hydrolase family 86 beta-agarase from a deep-sea Microbulbifer-like isolate.

The gene for a novel beta-agarase from a deep-sea Microbulbifer-like isolate was cloned and sequenced. It encoded a mature protein of 126,921 Da (1146 amino acids), which was a modular protein including two tandem carbohydrate-binding module (CBM)-like sequences and a catalytic module. The catalytic module resembled a glycoside hydrolase family 86 beta-agarase, AgrA, from Pseudoalteromonas atlantica T6c with 31% amino acid identity. Its recombinant agarase was hyper-produced extracellularly using Bacillus subtilis as the host and purified to homogeneity. The activity and stability were strongly enhanced by CaCl2. The maximal enzyme activity was observed at 45 degrees C and pH 7.5 in the presence of 10 mM CaCl2. The enzyme was an endo-type beta-agarase and degraded agarose and agarose oligosaccharides more polymerized than hexamers to yield neoagarohexaose as the main product. This is the first glycoside hydrolase family 86 enzyme to be homogeneously purified and characterized.

Alteromonadaceae↗