| 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 ... | 2001 | 11703190 |
| idiomarina loihiensis sp. nov., a halophilic gamma-proteobacterium from the lō'ihi submarine volcano, hawai'i. | during an investigation of bacterial diversity at hydrothermal vents on the lō'ihi seamount, hawai'i, a novel bacterium (designated l2-tr(t)) was cultivated, which shares 99.9 % 16s rrna gene sequence similarity over 1415 nt with an uncultured eubacterium from sediment at a depth of 11 000 m in the mariana trench. the nearest cultivated neighbour of l2-tr(t), however, is idiomarina abyssalis kmm 227(t), with which it shares 98.9 % 16s rrna sequence similarity. l2-tr(t) differed from i. abyssalis ... | 2003 | 14657116 |
| structure of the o-polysaccharide of idiomarina zobellii kmm 231t containing two unusual amino sugars with the free amino group, 4-amino-4,6-dideoxy-d-glucose and 2-amino-2-deoxy-l-guluronic acid. | mild acid degradation of the lipopolysaccharide of the bacterium idiomarina zobellii, type strain kmm 231t, with aq 2% hoac at 100 degrees c, yielded an oligosaccharide, which represents one repeating unit of the o-polysaccharide. a polysaccharide was obtained by mild base degradation of the lipopolysaccharide. the following structure of the o-polysaccharide was elucidated by 1h and 13c nmr spectroscopy of the oligosaccharide and base-degraded lipopolysaccharide, including cosy, tocsy, roesy, 1h ... | 2004 | 15013384 |
| [phylogenetic diversity of culturable bacteria in the ancient salt deposits of the yipinglang salt mine, p. r. china]. | the microbial diversity of cultivable bacteria, isolated from the ancient salt deposits from the yipinglang salt mine (ypl) in the yunnan province, p. r. china,was investigated by using conventional culture-dependent method and phylogenetic analyses based on 16s rrna gene sequence comparisons. 38 bacteria strains were isolated from the brine, halite and saline soil samples on mba (marine broth agar 2216, difco) and isp 2 (international streotomyces project medium 2) media supplemented with 0.5-3 ... | 2007 | 17944352 |
| characterization of exopolysaccharides produced by three moderately halophilic bacteria belonging to the family alteromonadaceae. | to study the exopolysaccharides (epss) produced by three novel moderately halophilic species belonging to the family alteromonadaceae to optimize eps yields, characterize their physical and chemical properties and evaluate possible biotechnological applications for these polymers. | 2008 | 18540968 |
| comparing patterns of natural selection across species using selective signatures. | comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. in the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and ... | 2008 | 18266472 |
| idiomarina salinarum sp. nov., isolated from a marine solar saltern in korea. | a gram-negative, motile, rod-shaped, idiomarina-like bacterial strain, isl-52t, was isolated from a marine solar saltern of the yellow sea in korea and was subjected to a polyphasic taxonomic investigation. strain isl-52t grew optimally at ph 7.0-8.0 and at 30-37 degrees c. it contained q-8 as the predominant ubiquinone. the major fatty acids (>10% of total fatty acids) were iso-c15:0, iso-c17:0 and iso-c17:1omega9c. the dna g+c content was 53.9 mol%. a phylogenetic analysis based on 16s rrna ge ... | 2007 | 17978209 |
| solving ambiguities in contig assembly of idiomarina loihiensis l2tr chromosome by in silico analyses. | nucleotide composition analyses of bacterial genomes such as cumulative gc skew highlight the atypical, strongly asymmetric architecture of the recently published chromosome of idiomarina loihiensis l2tr, suggesting that an inversion of a 600-kb chromosomal segment occurred. the presence of 3.4-kb inverted repeated sequences at the borders of the putative rearrangement supports this hypothesis. reverting in silico this segment restores (1) a symmetric chromosome architecture; (2) the co-orientat ... | 2007 | 17442016 |
| phylogenetic analysis of a biofilm bacterial population in a water pipeline in the gulf of mexico. | the aim of this study was to assess the bacterial diversity associated with a corrosive biofilm in a steel pipeline from the gulf of mexico used to inject marine water into the oil reservoir. several aerobic and heterotrophic bacteria were isolated and identified by 16s rrna gene sequence analysis. metagenomic dna was also extracted to perform a denaturing gradient gel electrophoresis analysis of ribosomal genes and to construct a 16s rrna gene metagenomic library. denaturing gradient gel electr ... | 2006 | 16958915 |
| idiomarina homiensis sp. nov., isolated from seashore sand in korea. | a halophilic, aerobic bacterium, designated po-m2(t), was isolated from seashore sand, from pohang, korea and characterized on the basis of physiological and biochemical features. phylogenetic analysis of 16s rrna gene sequences revealed a clear affiliation of the novel strain with members of the genus idiomarina. sequence similarities between strain po-m2(t) and the type strains of species belonging to the genus idiomarina ranged from 94.3 to 95.5 %. cells of strain po-m2(t) were straight or sl ... | 2006 | 16957126 |
| bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of n-acetylated intermediates in prokaryotes. | the n-acetylation of l-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical n-acetylglutamate synthase (nags, gene arga) first characterized in escherichia coli and pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (oat, gene argj) present in bacteria, a ... | 2006 | 16409639 |
| ecophysiology and molecular phylogeny of bacteria isolated from alkaline two-phase olive mill wastes. | the use of two-phase centrifugal decanters has been widely adopted in the olive oil extraction industry in order to reduce the huge quantities of wastewaters produced during the traditional three-phase extraction process. the resulting sludge-like byproduct, widely known as "alpeorujo", has a ph of 4-6, low water activity (a(w)) and high phytotoxicity. addition of ca(oh)(2) to alpeorujo, which is commonly performed at the olive oil mill to handle disposal problems related to acidic ph and odor e ... | 2006 | 16307869 |
| flagellar filaments of the deep-sea bacteria idiomarina loihiensis belong to a family different from those of salmonella typhimurium. | the helical filaments of the bacterial flagella so far studied seem to be universal in the bacterial kingdom. despite the variation in flagellin molecular masses, which range from 24 kda to 62 kda in different species, there are only two forms: either the so-called normal (left-handed) or the curly (right-handed). the normal and curly helical forms are asymmetric; the two characteristic helical parameters, which are the pitch and diameter, of normal filaments are twice those of curly filaments. ... | 2005 | 16120444 |
| halotolerant aerobic heterotrophic bacteria from the great salt plains of oklahoma. | the salt plains national wildlife refuge (spnwr) near cherokee, oklahoma, contains a barren salt flat where permian brine rises to the surface and evaporates under dry conditions to leave a crust of white salt. rainfall events dissolve the salt crust and create ephemeral streams and ponds. the rapidly changing salinity and high surface temperatures, salinity, and uv exposure make this an extreme environment. the salt plains microbial observatory (spmo) examined the soil microbial community of th ... | 2004 | 15696379 |
| idiomarina seosinensis sp. nov., isolated from hypersaline water of a solar saltern in korea. | a halophilic gamma-proteobacterium, designated cl-sp19t, was isolated from hypersaline water from a solar saltern located in seosin, korea. analysis of the 16s rrna gene sequence revealed an affiliation with the genus idiomarina. the sequence similarities between cl-sp19t and type strains of the genus idiomarina ranged from 95.9 to 96.9 %. cells were straight or slightly curved rods and were motile by means of a single polar flagellum. the major fatty acids were c(15 : 0) iso (17.1 %) and c(17 : ... | 2005 | 15653904 |
| genome sequence of the deep-sea gamma-proteobacterium idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. | we report the complete genome sequence of the deep-sea gamma-proteobacterium, idiomarina loihiensis, isolated recently from a hydrothermal vent at 1,300-m depth on the loihi submarine volcano, hawaii. the i. loihiensis genome comprises a single chromosome of 2,839,318 base pairs, encoding 2,640 proteins, four rrna operons, and 56 trna genes. a comparison of i. loihiensis to the genomes of other gamma-proteobacteria reveals abundance of amino acid transport and degradation enzymes, but a loss of ... | 2004 | 15596722 |
| idiomarina fontislapidosi sp. nov. and idiomarina ramblicola sp. nov., isolated from inland hypersaline habitats in spain. | two bacterial strains, f23t and r22t, have been isolated from hypersaline habitats in málaga (s. spain) and murcia (e. spain). the novel strains, similar to previously described idiomarina species, are slightly curved rods, gram-negative, chemo-organotrophic, strictly aerobic and motile by a single polar flagellum. both strains produce catalase and oxidase. they hydrolyse aesculin, gelatin, casein, tween 20, tween 80 and dna but not starch or tyrosine. the strains differ from the hitherto descri ... | 2004 | 15388745 |
| 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 studie ... | 2004 | 15388743 |
| idiomarina baltica sp. nov., a marine bacterium with a high optimum growth temperature isolated from surface water of the central baltic sea. | two bacterial strains isolated from the baltic sea, os145t and os146, were characterized on the basis of their physiological and biochemical features, their fatty acid profiles and their phylogenetic position based on 16s rdna sequence analyses. the strains were isolated from the upperoxic water column of the central baltic sea. phylogenetic analyses of the 16s rdna gene sequences revealed a clear affiliation of the novel strains with members of the genus idiomarina, of the gammaproteobacteria. ... | 2003 | 12710605 |
| [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 ... | 2001 | 11338830 |
| evaluation of phospholipid and fatty acid compositions as chemotaxonomic markers of alteromonas-like proteobacteria. | the cellular phospholipids (pls) and fatty acids (fas) were investigated in type and environmental strains of pseudoalteromonas, alteromonas macleodii, a. infernus, and in three type strains of marinomonas, m. communis, m. vaga, m. mediterranea. a total of 40 strains (19 strains in this study and 21 reported in previous papers), including idiomarina abyssalis, i. zobellii, and glaciecola punicea, g. pallidula, aerobic alteromonas-like proteobacteria showed genus-characteristic patterns of phosph ... | 2000 | 11014871 |
| idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the pacific ocean, including descriptions of two species, idiomarina abyssalis sp. nov. and idiomarina zobellii sp. nov. | two bacterial strains, kmm 227t and 231t, were isolated from seawater samples collected from the north-western pacific ocean at a depth of 4000-5000 m and were characterized using polyphasic taxonomy. both were gram-negative, psychrotolerant, heterotrophic, aerobic and required nacl for growth (0.6-15.0%). the temperature for growth was 4-30 degrees c. both strains were rod-shaped, with a single flagellum. however, strain kmm 231t revealed a single long fimbrium. cellular fatty acids detected in ... | 2000 | 10758902 |
| locked chromophore analogs reveal that photoactive yellow protein regulates biofilm formation in the deep sea bacterium idiomarina loihiensis. | idiomarina loihiensis is a heterotrophic deep sea bacterium with no known photobiology. we show that light suppresses biofilm formation in this organism. the genome of i. loihiensis encodes a single photoreceptor protein: a homologue of photoactive yellow protein (pyp), a blue light receptor with photochemistry based on trans to cis isomerization of its p-coumaric acid (pca) chromophore. the addition of trans-locked pca to i. loihiensis increases biofilm formation, whereas cis-locked pca decreas ... | 2009 | 19891493 |
| bacterial diversity of marine seeps in the southeastern gulf of mexico. | the diversity of bacterial communities of shallow (< or = 100 m depth) oil seep marine sediments from the southern gulf of mexico was evaluated. the geochemical properties of seep sediments were characterized as well as their microbial diversity in oil seep and control sediments. bacteria were identified through molecular tools as belonging to the genera marinobacter, idiomarina, marinobacterium, frauteria and an unknown bacterium. bacteria might be important components of microbial communities ... | 2009 | 19634471 |
| description of idiomarina insulisalsae sp. nov., isolated from the soil of a sea salt evaporation pond, proposal to transfer the species of the genus pseudidiomarina to the genus idiomarina and emended description of the genus idiomarina. | a halophilic, aerobic gram-negative bacterium, designated strain cvs-6(t), was isolated from a sea salt evaporation pond on the island of sal in the cape verde archipelago. phylogenetic analysis of the 16s rrna gene sequence revealed a clear affiliation of the organism with members of the family idiomarinaceae. sequence similarities between cvs-6(t) and the type strains of the species of the genera pseudidiomarina and idiomarina ranged from 93.7% to 96.9%. the major isoprenoid quinone was ubiqui ... | 2009 | 19625151 |
| diversity of both the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the south china sea. | protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. in this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the south china sea was investigated. the richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. analysis of the 16s rrna gene se ... | 2009 | 19301066 |
| pseudidiomarina marina sp. nov. and pseudidiomarina tainanensis sp. nov. and reclassification of idiomarina homiensis and idiomarina salinarum as pseudidiomarina homiensis comb. nov. and pseudidiomarina salinarum comb. nov., respectively. | two gram-negative strains of heterotrophic, aerobic, marine bacteria, designated pim1t and pin1t, were isolated from seawater samples collected from the shallow coastal region of an-ping harbour, tainan, taiwan. cells grown in broth cultures were straight rods and non-motile. the two isolates required nacl for growth and grew optimally at 30-35 degrees c and 2-5 % nacl. they grew aerobically and were not capable of anaerobic growth by fermentation of glucose or other carbohydrates. the cellular ... | 2009 | 19126723 |
| characterization of a deep-sea sediment metagenomic clone that produces water-soluble melanin in escherichia coli. | to access to the microbial genetic resources of deep-sea sediment by a culture-independent approach, the sediment dna was extracted and cloned into fosmid vector (pcc1fos) generating a library of 39,600 clones with inserts of 24-45 kb. the clone fss6 producing red-brown pigment was isolated and characterized. the pigment was identified as melanin according to its physico-chemical characteristics. subcloning and sequences analyses of fss6 demonstrated that one open reading frame (orf2) was respon ... | 2009 | 18648877 |
| polar, peritrichous, and lateral flagella belong to three distinguishable flagellar families. | the bacterial flagellum transforms its shape into several distinguishable helical shapes (polymorphs) under various environmental conditions. polymorphs of each type of flagellum stay on a circle in the pitch-diameter (p versus pid) plot, indicating that they all belong to one family. previously, we showed that the flagellar family of a marine bacterium idiomarina loihiensis (family ii) differed from the conventional flagellar family of salmonella typhimurium (family i). the pitch and diameter o ... | 2008 | 18455187 |
| ca-mg kutnahorite and struvite production by idiomarina strains at modern seawater salinities. | the production of mg-rich carbonates by idiomarina bacteria at modern seawater salinities has been investigated. with this objective, four strains: idiomarina abyssalis (strain atcc baa-312), idiomarina baltica (strain dsm 15154), idiomarina loihiensis (strains dsm 15497 and mah1) were used. the strain i. loihiensis mah1 is a new isolate, identified in the scope of this work. the four moderately halophilic strains precipitated struvite (nh4mgpo4 x 6h2o) crystals that appear encased by small ca-m ... | 2008 | 18355891 |
| gene diversity of cyp153a and alkb alkane hydroxylases in oil-degrading bacteria isolated from the atlantic ocean. | alkane hydroxylases, including the integral-membrane non-haem iron monooxygenase (alkb) and cytochrome p450 cyp153 family, are key enzymes in bacterial alkane oxidation. although both genes have been detected in a number of bacteria and environments, knowledge about the diversity of these genes in marine alkane-degrading bacteria is still limited, especially in pelagic areas. in this report, 177 bacterial isolates, comprising 43 genera, were obtained from 18 oil-degrading consortia enriched from ... | 2010 | 20148932 |
| isolation and characterisation of bacteria from the haloalkaline lake elmenteita, kenya. | culture-independent studies show that soda lake environments harbour diverse groups of bacteria and archaea. in this study different enrichment and isolation media were used in an attempt to isolate novel groups of bacteria from lake elmenteita. different media were prepared using filter-sterilised water from the lake. the isolates recovered were purified on tryptic soy agar supplemented with 1% sodium carbonate and 4% sodium chloride. phylogenetic analysis of 181 partial 16s rrna gene sequences ... | 2010 | 20401502 |
| idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer pseudidiomarina aestuarii to the genus idiomarina as idiomarina aestuarii comb. nov. | a taxonomic study was carried out on strain 10-d-4(t), which was isolated from a crude oil-degrading consortium enriched from surface seawater collected around xiamen island, pr china. strain 10-d-4(t) grew optimally at ph 7.0-8.0 and at 25 °c. the 16s rrna gene sequence of strain 10-d-4(t) showed the highest similarity to those of idiomarina salinarum isl-52(t) (94.6 %), idiomarina tainanensis pin1(t) (94.2 %) and idiomarina seosinensis cl-sp19(t) (94.1 %), and showed lower similarity (92.3-94. ... | 2011 | 20511464 |
| identities of epilithic hydrocarbon-utilizing diazotrophic bacteria from the arabian gulf coasts, and their potential for oil bioremediation without nitrogen supplementation. | gravel particles from four sites along the arabian gulf coast in autumn, winter, and spring were naturally colonized with microbial consortia containing between 7 and 400 × 10(2) cm(-2) of cultivable oil-utilizing bacteria. the 16s rrna gene sequences of 70 representatives of oil-utilizing bacteria revealed that they were predominantly affiliated with the gammaproteobacteria and the actinobacteria. the gammaproteobacteria comprised among others, the genera pseudomonas, pseudoalteromonas, shewane ... | 2010 | 20567813 |
| microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. | marine dissolved organic matter (dom) contains as much carbon as the earth's atmosphere, and represents a critical component of the global carbon cycle. to better define microbial processes and activities associated with marine dom cycling, we analyzed genomic and transcriptional responses of microbial communities to high-molecular-weight dom (hmwdom) addition. the cell density in the unamended control remained constant, with very few transcript categories exhibiting significant differences over ... | 2010 | 20807744 |
| aliidiomarina taiwanensis gen. nov., sp. nov., a marine bacterium isolated from shallow coastal water from bitou harbour, taiwan. | a gram-negative, heterotrophic, aerobic, marine bacterium, designated strain ait1(t), was isolated from a seawater sample collected in the shallow coastal region of bitou harbour, taipei county, taiwan. cells grown in broth cultures were straight to slightly curved rods that were motile by means of a single polar flagellum. strain ait1(t) required nacl for growth and grew optimally at 30-40°c and 1.5-5% nacl. it grew aerobically and was incapable of anaerobic growth by fermentation of glucose or ... | 2011 | 21378139 |
| idiomarina maris sp. nov., a marine bacterium isolated from sediment of the south china sea. | a protease-producing marine bacterium, designated strain cf12-14(t), was isolated from the sediment of the south china sea. phylogenetic analyses of 16s rrna gene sequences revealed that strain cf12-14(t) formed a separate lineage within the genus idiomarina (gammaproteobacteria). it showed highest sequence similarities to type strains of idiomarina salinarum (94.7 %) and idiomarina seosinenesis (94.6 %) and 91.9-94.6 % sequence similarities to those of other idiomarina species. cells of strain ... | 2011 | 21441375 |
| biological treatment of refinery spent caustics under halo-alkaline conditions. | the present research demonstrates the biological treatment of refinery sulfidic spent caustics in a continuously fed system under halo-alkaline conditions (i.e. ph 9.5; na(+)= 0.8m). experiments were performed in identical gas-lift bioreactors operated under aerobic conditions (80-90% saturation) at 35°c. sulfide loading rates up to 27mmoll(-1)day(-1) were successfully applied at a hrt of 3.5days. sulfide was completely converted into sulfate by the haloalkaliphilic sulfide-oxidizing bacteria be ... | 2011 | 21602041 |
| a preliminary study of the microbial resources and their biological activities of the east china sea. | east china sea is one of the four sea areas in china, which possesses peculiar ecological environment and many kinds of living creatures, especially the microorganisms. we established the east china sea microorganism library (during 2006-2010) for the first time, which stored about 30000 strains that covered most kinds of the species. in this paper, 395 pure strains of east china sea microorganism library which belong to 33 different genera were mainly introduced. sulfitobacter, halomonas, bacil ... | 2011 | 21789045 |
| genome sequence of idiomarina sp. strain a28l, isolated from pangong lake, india. | idiomarina sp. strain a28l was isolated from alkaline brackish water of high altitude pangong lake. here we present, a draft genome of idiomarina sp. strain a28l that contain 2,591,567 bp with a 45.5 mol percent dna g+c content and contain 2299 protein coding genes and 56 structural rnas. | 2011 | 21742887 |
| idiomarina aquimaris sp. nov., isolated from the reef-building coral isopora palifera. | a bacterial strain designated sw15t was isolated from the reef-building coral isopora palifera, collected from southern taiwan and was characterized using a polyphasic taxonomic approach. strain sw15t was gram-negative, aerobic, light yellowish colored, rod-shaped, and motile by monopolar flagellum. phylogenetic analyses based on 16s rrna gene sequences showed that strain sw15t belonged to the genus idiomarina in the gammaproteobacteria. sequence similarities to type strains of the genus idiomar ... | 2011 | 21856977 |
| the structural diversity of carbohydrate antigens of selected gram-negative marine bacteria. | marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. among these biologically active molecules, t ... | 2011 | 22073003 |