Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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| rrna-targeted fluorescent in situ hybridization analysis of bacterial community structure in river water. | an improved in situ hybridization technique, hnpp-fish, using 2-hydroxy-3-naphthoic acid 2'-phenylanilide phosphate (hnpp) and fast red tr was applied to analyse the community structure of planktonic bacteria in river water. oligonucleotide probes specific for the domain bacteria (eub338) and five bacterial groups [flavobacterium-cytophaga; burkholderia-pseudomonas (rrna iii)-authentic alcaligenes; vibrio-aeromonas; pseudomonas (rrna i): the genus acinetobacter] were used to investigate the bact ... | 1998 | 9720029 |
| genetic diversity of the biofilm covering montacuta ferruginosa (mollusca, bivalvia) as evaluated by denaturing gradient gel electrophoresis analysis and cloning of pcr-amplified gene fragments coding for 16s rrna. | the shell of the bivalve montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. this biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. the aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their ... | 1998 | 9726898 |
| a gliding bacterium strain inhibits adhesion and motility of another gliding bacterium strain in a marine biofilm | two species of gliding bacteria were isolated from a marine biofilm. they were described and identified as members of the genus cytophaga. one of them (rb1057) produced an extracellular inhibitor of colony expansion of the other (rb1058). the inhibitor was characterized as a glycoprotein with an apparent molecular mass of 60 kda. it inhibited rb1058 adhesion to and gliding on substrata. motility and adhesion of several other aquatic gliding bacteria were not measurably affected by this agent. | 1998 | 9758848 |
| molecular characterization of epiphytic bacterial communities on charophycean green algae | epiphytic bacterial communities within the sheath material of three filamentous green algae, desmidium grevillii, hyalotheca dissiliens, and spondylosium pulchrum (class charophyceae, order zygnematales), collected from a sphagnum bog were characterized by pcr amplification, cloning, and sequencing of 16s ribosomal dna. a total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. by phyloge ... | 1998 | 9797295 |
| in situ detection of bacteria in continuous-flow cultures of seawater sediment suspensions with fluorescently labelled rrna-directed oligonucleotide probes. | rrna-targeted and fluorescently labelled oligonucleotide probes were used to study the composition of natural bacterial populations in continuous-flow cultures of seawater sediment suspensions. the cultures were run as enrichment cultures with increasing dilution rates, and hexadecane as the sole carbon source. total cell numbers were analysed by counting dapi (4',6-diamidino-2-phenylindole)-stained cells. to differentiate the population composition, oligonucleotide probes for eubacteria, for cy ... | 1998 | 9802019 |
| pharmacokinetics of oxytetracycline in the red pacu (colossoma brachypomum) following different routes of administration. | oxytetracycline (otc) pharmacokinetics were studied in the red pacu (colossoma brachypomum) following intravenous (i.v.) and intramuscular (i.m.) administration at a dose of 5 mg/kg body weight. otc plasma concentrations were determined by high-performance-liquid-chromatography (hplc). a non-compartmental model was used to describe plasma drug disposition after otc administration. following i.m. administration, the elimination half-life (t1/2) was 62.65 +/- 1.25 h and the bioavailability was 49. ... | 1998 | 9811436 |
| protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. | the presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. an alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. in this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryote ... | 1998 | 9841678 |
| purification and properties of arfi, an alpha-l-arabinofuranosidase from cytophaga xylanolytica. | an alpha-l-arabinofuranosidase (alpha-l-arabinofuranoside arabinofuranohydrolase [ec 3.2.1.55]; referred to below as arfi) from cytophaga xylanolytica xm3 was purified 85-fold by anion-exchange and hydrophobic interaction column chromatography. the native enzyme had a pi of 6.1 and an apparent molecular mass of 160 to 210 kda, and it appeared to be a trimer or tetramer consisting of 56-kda subunits. with p-nitrophenyl-alpha-l-arabinofuranoside as the substrate, the enzyme exhibited a k(m) of 0.5 ... | 1998 | 9435061 |
| arfi and arfii, two genes encoding alpha-l-arabinofuranosidases in cytophaga xylanolytica. | arfi encoded the 57.7-kda subunit of cytophaga xylanolytica arabinofuranosidase i (arfi). arfii encoded a 59.2-kda subunit of arfii. products of both cloned genes liberated arabinose from arabinan and arabinoxylan. the deduced amino acid sequences of arfi and arfii revealed numerous regions that were identical to each other and to regions of homologous proteins from bacteroides ovatus, bacillus subtilis, and clostridium stercorarium. | 1998 | 9572972 |
| the kappa-carrageenase of the marine bacterium cytophaga drobachiensis. structural and phylogenetic relationships within family-16 glycoside hydrolases. | we report here cloning from the marine gliding bacterium cytophaga drobachiensis of kappa-carrageenase, a glycoside hydrolase involved in the degradation of kappa-carrageenan. structural features in the nucleotide sequence are pointed out, including the presence of an octameric omega sequence similar to the ribosome-binding sites of various eukaryotes and prokaryotes. the cgka gene codes for a protein of 545 aa, with a signal peptide of 35 aa and a 229-aa-long posttranslationaly processed c-term ... | 1998 | 9580981 |
| the phylogenetic relationships of chlorobium tepidum and chloroflexus aurantiacus based upon their reca sequences. | using reca as the phylogenetic marker, the relationships of the green sulfur bacterium chlorobium tepidum and the green non-sulfur bacterium chloroflexus aurantiacus to other eubacteria were investigated. the reca genes of the two organisms were cloned, and the resulting protein sequences aligned with 86 other eubacterial reca sequences. cb. tepidum was placed as the nearest relative to the cytophaga/flexibacter/bacteriodes group, a relationship supported by results obtained with several phyloge ... | 1998 | 9595663 |
| microbial community composition of wadden sea sediments as revealed by fluorescence in situ hybridization. | the microbial community composition of wadden sea sediments of the german north sea coast was investigated by in situ hybridization with group-specific fluorescently labeled, rrna-targeted oligonucleotides. a large fraction (up to 73%) of the dapi (4',6-diamidino-2-phenylindole)-stained cells hybridized with the bacterial probes. nearly 45% of the total cells could be further identified as belonging to known phyla. members of the cytophaga-flavobacterium cluster were most abundant in all layers, ... | 1998 | 9647850 |
| processing respiratory specimens with c18-carboxypropylbetaine: development of a sediment resuspension buffer that contains lytic enzymes to reduce the contamination rate and lecithin to alleviate toxicity. | the c18-carboxypropylbetaine (cb-18) procedure for processing respiratory specimens for the detection of mycobacteria was shown to provide significant increases in sensitivity by smear and culture. however, the procedure also produced increased contamination, a loss in liquid culture sensitivity, and a reduction in smear specificity. because of these observations, the toxicity of cb-18 and the nature of the contamination were characterized. preincubation in 1 mm cb-18 impacted viability in a tim ... | 1998 | 9650952 |
| phylogenetic heterogeneity within the genus herpetosiphon: transfer of the marine species herpetosiphon cohaerens, herpetosiphon nigricans and herpetosiphon persicus to the genus lewinella gen. nov. in the flexibacter-bacteroides-cytophaga phylum. | analysis of the 16s rdna sequences of species currently assigned to the genus herpetosiphon revealed intrageneric phylogenetic heterogeneity. the thermotolerant freshwater species herpetosiphon geysericola is most closely related to the type species herpetosiphon aurantiacus in the chloroflexus subdivision of the green non-sulfur bacteria. the marine species herpetosiphon cohaerens, herpetosiphon nigricans and herpetosiphon persicus, on the other hand, were found to form a cluster with sheathed ... | 1998 | 9734027 |
| polaribacter gen. nov., with three new species, p. irgensii sp. nov., p. franzmannii sp. nov. and p. filamentus sp. nov., gas vacuolate polar marine bacteria of the cytophaga-flavobacterium-bacteroides group and reclassification of 'flectobacillus glomeratus' as polaribacter glomeratus comb. nov. | several psychrophilic, gas vacuolate strains of the cytophage-flavobacterium-bacteroides (cfb) phylogenetic group were isolated from sea ice and water from the arctic and the antarctic. the closest taxonomically defined species by 16s rrna sequence analysis is 'flectobacillus glomeratus'. however, 'flc. glomeratus' is phylogenetically distant from the flectobacillus type species, flc. major. on the basis of phenotypic, genotypic and 16s rrna sequence analyses we propose a new genus, polaribacter ... | 1998 | 9542092 |
| seasonal community and population dynamics of pelagic bacteria and archaea in a high mountain lake | the seasonal variations in community structure and cell morphology of pelagic procaryotes from a high mountain lake (gossenkollesee, austria) were studied by in situ hybridization with rrna-targeted fluorescently labeled oligonucleotide probes (fish) and image-analyzed microscopy. compositional changes and biomass fluctuations within the assemblage were observed both in summer and beneath the winter ice cover and are discussed in the context of physicochemical and biotic parameters. proteobacter ... | 1998 | 9797280 |
| hymenobacter roseosalivarius gen. nov., sp. nov. from continental antartica soils and sandstone: bacteria of the cytophaga/flavobacterium/bacteroides line of phylogenetic descent. | aseptically collected sandstone and soil samples from the antarctic dry valleys were inoculated into oligotrophic media and incubated under low light intensities. a total of 41 gram-negative isolates were obtained with reddish colonies spreading on agar. a sandstone isolate and four soil strains were characterized further. they were nearly identical in morphological, physiological, biochemical and chemotaxonomic properties. they produced large amounts of extracellular polymer and utilized for gr ... | 1998 | 9841127 |
| microbial diversity in sediments collected from the deepest cold-seep area, the japan trench. | : the japan trench land slope at a depth of 6,400 m is the deepest cold-seep environment with calyptogena communities. sediment samples from inside and beside the calyptogena communities were collected, and the microbial diversity in the sediment samples was studied by molecular phylogenetic techniques. from dna extracted directly from the sediment samples, 16s rdnas were amplified by the polymerase chain reaction method. the sequences of the amplified 16s rdnas selected by restriction fragment ... | 1999 | 10489418 |
| phylogeny and in situ identification of a morphologically conspicuous bacterium, candidatus magnospira bakii, present at very low frequency in activated sludge. | a morphologically conspicuous bacterium that constituted a very small fraction (< 0.01%) of the total microbial community of activated sludge was enriched and analysed phylogenetically by a combination of cultivation-independent molecular and physical methods. the large, corkscrew-shaped, filamentous bacteria were first detected in municipal activated sludge by light microscopy owing to their unusual rotating gliding motility. various attempts at microbiological enrichment and pure culture isola ... | 1999 | 11207728 |
| bacterial filament formation, a defense mechanism against flagellate grazing, is growth rate controlled in bacteria of different phyla. | a facultatively filamentous bacterium was isolated from eutrophic lake water and was identified as flectobacillus sp. strain mwh38 (a member of the cytophaga-flavobacterium-bacteroides phylum) by comparative 16s rrna gene sequence analysis. filament formation by flectobacillus sp. strain mwh38 and filament formation by flectobacillus major, the closest known relative of strain mwh38, were studied in chemostat cultures under grazing pressure by the bacterivorous flagellate ochromonas sp. strain d ... | 1999 | 9872755 |
| morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. | we analyzed changes in bacterioplankton morphology and composition during enhanced protozoan grazing by image analysis and fluorescent in situ hybridization with group-specific rrna-targeted oligonucleotide probes. enclosure experiments were conducted in a small, fishless freshwater pond which was dominated by the cladoceran daphnia magna. the removal of metazooplankton enhanced protozoan grazing pressure and triggered a microbial succession from fast-growing small bacteria to larger grazing-res ... | 1999 | 10049890 |
| combined microautoradiography-16s rrna probe technique for determination of radioisotope uptake by specific microbial cell types in situ. | we propose a novel method for studying the function of specific microbial groups in situ. since natural microbial communities are dynamic both in composition and in activities, we argue that the microbial "black box" should not be regarded as homogeneous. our technique breaks down this black box with group-specific fluorescent 16s rrna probes and simultaneously determines 3h-substrate uptake by each of the subgroups present via microautoradiography (mar). total direct counting, fluorescent in si ... | 1999 | 10103276 |
| diversity of chlorophenol-degrading bacteria isolated from contaminated boreal groundwater. | chlorophenol-degrading bacteria from a long-term polluted groundwater aquifer were characterized. all isolates degraded 2,4,6-trichlorophenol and 2,3,4,6-tetrachlorophenol at concentrations detected in the contaminated groundwater (< 10 mg 1(-1)). pentachlorophenol was degraded by three isolates when present alone. in two gram-positive isolates, 2,3,4,6-tetrachlorophenol was required as an inducer for the degradation of pentachlorophenol. the gram-positive isolates were sensitive to pentachlorop ... | 1999 | 10201097 |
| an improved growth medium for flavobacterium psychrophilum. | supplementing cytophaga agar and broth with 0.5 g l-1 each of d(+) galactose, d(+) glucose, l-rhamnose and skimmed milk gave a dramatic improvement in the isolation of the fish pathogen flavobacterium psychrophilum. by means of spread-plating, approximately double the number of colonies of larger size were obtained on the improved medium compared to cytophaga agar alone. in supplemented cytophaga broth, growth of fl. psychrophilum was more rapid and generated greater biomass. | 1999 | 10212443 |
| phylogenetic position of chitinophaga pinensis in the flexibacter-bacteroides-cytophaga phylum. | comparison of the 16s rrna gene sequence determined for chitinophaga pinensis showed that this species is most closely related to flexibacter filiformis in the flexibacter-bacteroides-cytophaga phylum. these two chitinolytic bacteria, which are characterized by transformation into spherical bodies on ageing, belong to a strongly supported lineage that also includes cytophaga arvensicola, flavobacterium ferrugineum and flexibacter sancti. the lineage is distinct from the microcyst-forming species ... | 1999 | 10319467 |
| coenonia anatina gen. nov., sp. nov., a novel bacterium associated with respiratory disease in ducks and geese. | taxon 1502 was originally described as a riemerella anatipestifer-like bacterium causing exudative septicaemia in ducks and geese. in the present study, an integrated genotypic and phenotypic approach was used to elucidate the phylogenetic affiliation and taxonomic relationships of 12 strains of taxon 1502. whole-cell protein and fatty acid analyses and an extensive biochemical examination by using conventional tests and several api microtest systems indicated that all isolates formed a homogene ... | 1999 | 10319512 |
| phylogenetic composition, spatial structure, and dynamics of lotic bacterial biofilms investigated by fluorescent in situ hybridization and confocal laser scanning microscopy. | > abstract the phylogenetic composition, three-dimensional structure and dynamics of bacterial communities in river biofilms generated in a rotating annular reactor system were studied by fluorescent in situ hybridization (fish) and confocal laser scanning microscopy (clsm). biofilms grew on independently removable polycarbonate slides exposed in the reactor system with natural river water as inoculum and sole nutrient and carbon source. the microbial biofilm community developed from attached si ... | 1999 | 10341052 |
| evolutionary relationships among photosynthetic prokaryotes (heliobacterium chlorum, chloroflexus aurantiacus, cyanobacteria, chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. | the presence of shared conserved insertions or deletions in proteins (referred to as signature sequences) provides a powerful means to deduce the evolutionary relationships among prokaryotic organisms. this approach was used in the present work to deduce the branching orders of various eubacterial taxa consisting of photosynthetic organisms. for this purpose, portions of the hsp60 and hsp70 genes, covering known signature sequence regions, were pcr-amplified and sequenced from heliobacterium chl ... | 1999 | 10361294 |
| phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. | the columbia river estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. pcr-amplified 16s rrna genes from particle-attached and free-living bacteria in the columbia river, its estuary, and the adjacent coastal ocean were cloned, and 239 ... | 1999 | 10388721 |
| determination of total protein content of bacterial cells by sypro staining and flow cytometry. | an assay has been developed for measuring protein biomass of marine planktonic bacteria by flow cytometry. the method was calibrated by using five species of bacteria (an arcobacter sp., a cytophaga sp., an oceanospirillum sp., a pseudoalteromonas sp., and a vibrio sp.) recently isolated from seawater samples and grown in culture at different temperatures. the intensity of sypro-protein fluorescence of these bacteria strongly correlated with their total protein content, measured by the bicinchon ... | 1999 | 10388732 |
| the response of the microbial community of marine sediments to organic carbon input under anaerobic conditions. | cyanobacterial biomass was added to anaerobic sediment to simulate the natural input of complex organic substrate that occurs in nature after algae blooms. sediments were incubated at 0 degree c, 8 degrees c and 24 degrees c for 13 days. community dynamics were measured by fluorescence in situ hybridisation (fish), denaturing gradient gel electrophoresis (dgge), and sequencing of 16s rdna pcr products. metabolic changes were followed by the analysis of total carbon mineralisation, sulfate reduct ... | 1999 | 10390875 |
| characterization of the bacterial community of a zinc-polluted soil. | the bacterial community of a zinc-contaminated soil (maatheide soil in lommel, belgium) was studied using cultivation as well as cultivation-independent techniques. colony-forming units (cfu) were determined by plating on media with or without metals. dominant isolates were characterized by fatty acid methyl ester analysis (fame analysis) and pcr fingerprinting using repetitive extragenic palindromic sequences as primers. dna was directly extracted from soil samples and used as a template for th ... | 1999 | 10420584 |
| description of cellulophaga baltica gen. nov., sp. nov. and cellulophaga fucicola gen. nov., sp. nov. and reclassification of [cytophaga] lytica to cellulophaga lytica gen. nov., comb. nov. | phenotypic data indicate that gliding, yellow/orange-pigmented, agar-digesting bacterial strains were members of the cytophaga-flavobacterium-bacteroides (cfb) group. the strains were isolated from the surface of the marine benthic macroalga fucus serratus l. and the surrounding seawater at three localities in danish waters. the bacteria were gram-negative, flexirubin-negative, aerobic, catalase-positive and oxidase-negative and were psychrophilic and halophilic. all strains utilized d-fructose, ... | 1999 | 10425785 |
| phylogeny of the defined murine microbiota: altered schaedler flora. | the "altered schaedler flora" (asf) was developed for colonizing germfree rodents with a standardized microbiota. the purpose of this study was to identify each of the eight asf strains by 16s rrna sequence analysis. three strains were previously identified as lactobacillus acidophilus (strain asf 360), lactobacillus salivarius (strain asf 361), and bacteroides distasonis (strain asf 519) based on phenotypic criteria. 16s rrna analysis indicated that each of the strains differed from its presump ... | 1999 | 10427008 |
| microbial population changes during bioremediation of an experimental oil spill. | three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. in situ microbial community structures were monitored by phospholipid fatty acid (plfa) analysis and 16s rdna pcr-denaturing gradient gel electrophoresis (dgge) to (i) identify the bacterial community members responsible for the decontamination ... | 1999 | 10427050 |
| bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. | fluorescence in situ hybridization (fish) with rrna-targeted oligonucleotide probes was used to investigate the phylogenetic composition of bacterioplankton communities in several freshwater and marine samples. an average of about 50% of the cells were detected by probes for the domains bacteria and archaea, and of these, about half could be identified at the subdomain level with a set of group-specific probes. beta subclass proteobacteria constituted a dominant fraction in freshwater systems, a ... | 1999 | 10427073 |
| gliding motility in bacteria: insights from studies of myxococcus xanthus. | gliding motility is observed in a large variety of phylogenetically unrelated bacteria. gliding provides a means for microbes to travel in environments with a low water content, such as might be found in biofilms, microbial mats, and soil. gliding is defined as the movement of a cell on a surface in the direction of the long axis of the cell. because this definition is operational and not mechanistic, the underlying molecular motor(s) may be quite different in diverse microbes. in fact, studies ... | 1999 | 10477310 |
| gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-trna synthetases. | in translation, separate aminoacyl-trna synthetases attach the 20 different amino acids to their cognate trnas, with the exception of glutamine. eukaryotes and some bacteria employ a specific glutaminyl-trna synthetase (glnrs) which other bacteria, the archaea (archaebacteria), and organelles apparently lack. instead, trna(gln) is initially acylated with glutamate by glutamyl-trna synthetase (glurs), then the glutamate moiety is transamidated to glutamine. lamour et al. [(1994) proc natl acad sc ... | 1999 | 10486006 |
| localization and identification of populations of phosphatase-active bacterial cells associated with activated sludge flocs. | abstract the majority of phosphatase (po(4)ase) activity detected in fresh aerobic activated sludge from a municipal wastewater treatment plant was associated with suspended floc material. po(4)ase activity appeared to be localized in discrete bacteria-containing areas of the floc matrix based on the distribution of nucleic acid-stained cells and precipitated fluorescent crystals produced as a result of reaction of the enzyme(s) with the artificial substrate elftrade mark-po(4). of the total flo ... | 1999 | 10541782 |
| characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. | most-probable-number (liquid serial dilution culture) counts were obtained for polysaccharolytic and saccharolytic fermenting bacteria in the anoxic bulk soil of flooded microcosms containing rice plants. the highest viable counts (up to 2.5 x 10(8) cells per g [dry weight] of soil) were obtained by using xylan, pectin, or a mixture of seven mono- and disaccharides as the growth substrate. the total cell count for the soil, as determined by using 4', 6-diamidino-2-phenylindole staining, was 4.8 ... | 1999 | 10543821 |
| comparative phylogenetic assignment of environmental sequences of genes encoding 16s rrna and numerically abundant culturable bacteria from an anoxic rice paddy soil. | we used both cultivation and direct recovery of bacterial 16s rrna gene (rdna) sequences to investigate the structure of the bacterial community in anoxic rice paddy soil. isolation and phenotypic characterization of 19 saccharolytic and cellulolytic strains are described in the accompanying paper (k.-j. chin, d. hahn, u. hengstmann, w. liesack, and p. h. janssen, appl. environ. microbiol. 65:5042-5049, 1999). here we describe the phylogenetic positions of these strains in relation to 57 environ ... | 1999 | 10543822 |
| poles apart: biodiversity and biogeography of sea ice bacteria. | this review introduces the subjects of bacterial biodiversity and biogeography. studies of biogeography are important for understanding biodiversity, the occurrence of threatened species, and the ecological role of free-living and symbiotic prokaryotes. a set of postulates is proposed for biogeography as a guide to determining whether prokaryotes are "cosmopolitan" (found in more than one geographic location on earth) or candidate endemic species. the term "geovar" is coined to define a geograph ... | 1999 | 10547690 |
| psychrotrophic bacteria from a coastal station in the ross sea (terra nova bay, antarctica). | seawater samples were collected from a fixed, coastal station in the terra nova bay at different depths during the xth oceanographic cruise in the 1994-95 antarctic summer. picoplanktonic abundance, estimated by direct counts in epifluorescence microscopy, ranged from 2.2 x 10(7) to 1.6 x 10(8) cells.l-1. the heterotrophic bacterial densities, evaluated on marine agar 2216 (difco) after incubation at +4 degrees c for 21 days, ranged from 2 x 10(3) to 4.5 x 10(6) cfu.l-1. the qualitative composit ... | 1999 | 10555207 |
| phylogenetic analysis of genus marinilabilia and related bacteria based on the amino acid sequences of gyrb and emended description of marinilabilia salmonicolor with marinilabilia agarovorans as its subjective synonym. | the detailed phylogenetic relationships for genus marinilabilia and related taxa were analysed by using dna gyrase b subunit gene (gyrb) sequences. anaerobic bacteria in the cytophaga-flavobacterium-bacteroides phylum, namely genera marinilabilia, bacteroides, rikenella, prevotella and porphyromonas and cytophaga fermentans, were clustered in the same branch and the facultative anaerobes marinilabilia and cytophaga fermentans formed a subcluster in the branch of the anaerobic bacteria. phylogene ... | 1999 | 10555336 |
| differential enumeration and in situ localization of microorganisms in the hindgut of the lower termite mastotermes darwiniensis by hybridization with rrna-targeted probes | we examined the abundance and spatial distribution of major phylogenetic groups of the domain bacteria in hindguts of the australian lower termite mastotermes darwiniensis by using in situ hybridization with group-specific, fluorescently labeled, rrna-targeted oligonucleotide probes. between 32.0 +/- 7.2% and 52.3 +/- 8.2% of the dapi-stained cells in different hindgut fractions were detected with probe eub338, specific for members of the domain bacteria. about 85% of the prokaryotic cells were ... | 1999 | 10591851 |
| intracellular bacteria of acanthamoebae resembling legionella spp. turned out to be cytophaga sp. | acanthamoeba sp. isolated from the drinking water system of a hospital harboured gram-negative bacteria multiplying inside phagosomes and within the cytoplasm of their host cells. according to their morphology demonstrated by electron microscopy they resembled llaps (legionella-like amoebal pathogens) but turned out to be cytophaga sp. as shown by a typical profile of cellular fatty acids obtained by means of gas-liquid chromatography. | 1999 | 10603658 |
| [the toxicity and interferon-inducing activity of the lipopolysaccharides of cytophaga sp. (strains 81 and 92)]. | the experiments on mice and cell culture of a kidney of green monkey vero have shown that lipopolysaccharides (lps) of the studied strains 81 and 92 of cytophaga sp. were nontoxic. they were less active as compared to lps of other gram-negative bacteria as to interferon-inducing activity. a comparative study of initial and dephosphorylated lps has shown that phosphate groups were not responsible for the interferon-inducing activity of lps of cytophaga genus representatives. | 1999 | 10707530 |
| influence of physiological factors on the lysis effect of cytophaga on the red microalga rhodella reticulata. | the influence of different factors on the lysis of the red microalga, rhodella reticulata, by cytophaga sp. lr2 was studied. the pathogenic bacterial strain was more resistant than the alga to the physiological parameters studied, which assured long-term survival of bacteria in algal cultures. cytophaga sp. lr2 infected r. reticulata at temperatures between 15 and 30 degrees c, in the illuminated as well as the non-illuminated cultures, at ph values between 5.0 and 9.0, and in the presence of na ... | 2000 | 10736006 |
| use of length heterogeneity pcr and fatty acid methyl ester profiles to characterize microbial communities in soil. | in length heterogeneity pcr (lh-pcr) a fluorescently labeled primer is used to determine the relative amounts of amplified sequences originating from different microorganisms. labeled fragments are separated by gel electrophoresis and detected by laser-induced fluorescence with an automated gene sequencer. we used lh-pcr to evaluate the composition of the soil microbial community. four soils, which differed in terms of soil type and/or crop management practice, were studied. previous data for mi ... | 2000 | 10742258 |
| natural assemblages of marine proteobacteria and members of the cytophaga-flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. | we used a method that combines microautoradiography with hybridization of fluorescent rrna-targeted oligonucleotide probes to whole cells (micro-fish) to test the hypothesis that the relative contributions of various phylogenetic groups to the utilization of dissolved organic matter (dom) depend solely on their relative abundance in the bacterial community. we found that utilization of even simple low-molecular-weight dom components by bacteria differed across the major phylogenetic groups and o ... | 2000 | 10742262 |
| phylogenetic characterization of a novel radiation-resistant bacterium from irradiated pork: description of hymenobacter actinosclerus sp. nov. | a phylogenetic analysis was performed on a red-pigmented, radiation-resistant, gram-negative, rod-shaped organism originating from irradiated pork. comparative 16s rrna gene sequencing showed the bacterium was a member of the cytophaga-flavobacterium-bacteroides line of descent and represents a new subline within the genus hymenobacter. a new species, hymenobacter actinosclerus, is described for this novel radiation-resistant bacterium. the type strain of hymenobacter actinosclerus is ccug 39621 ... | 2000 | 10758882 |
| dyadobacter fermentans gen. nov., sp. nov., a novel gram-negative bacterium isolated from surface-sterilized zea mays stems. | a gram-negative bacterium, designated ns114t, was isolated from duplicate treatments of surface-sterilized zea mays stems. the plants were grown in synthetic soil under greenhouse conditions and watered with fertilizer containing no nitrogen. strain ns114t could not be isolated from plants watered with the standard level or 20% (w/v) of the standard level of nitrogen. cells occurred as pairs in young cultures that attached to form angled arrangements in r2a broth and occasionally formed rounded, ... | 2000 | 10758885 |
| bacteroides acidifaciens sp. nov., isolated from the caecum of mice. | during studies of the bacterial flora in the intestines of mice, we isolated characteristic strains which lowered the ph of peptone-yeast broth containing fildes' digest. based on 16s rrna sequence comparison, these isolates were considered to belong to the bacteroides cluster in the bacteroides subgroup of the cytophaga-flavobacterium-bacteroides phylum, and were divided into two groups. their phenotypic characteristics, i.e. growth in 20% bile, aesculin hydrolysis, and glucose-6-phosphate dehy ... | 2000 | 10826798 |
| bacterial community structure and physiological state within an industrial phenol bioremediation system. | the structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. rapid community fingerprinting by pcr-based denaturing gradient gel electrophoresis (dgge) of 16s rdna indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclu ... | 2000 | 10831417 |
| culturability and in situ abundance of pelagic bacteria from the north sea. | the culturability of abundant members of the domain bacteria in north sea bacterioplankton was investigated by a combination of various cultivation strategies and cultivation-independent 16s rrna-based techniques. we retrieved 16s rrna gene (rdna) clones from environmental dnas and determined the in situ abundance of different groups and genera by fluorescence in situ hybridization (fish). a culture collection of 145 strains was established by plating on oligotrophic medium. isolates were screen ... | 2000 | 10877804 |
| extremely halophilic bacteria in crystallizer ponds from solar salterns. | it is generally assumed that hypersaline environments with sodium chloride concentrations close to saturation are dominated by halophilic members of the domain archaea, while bacteria are not considered to be relevant in this kind of environment. here, we report the high abundance and growth of a new group of hitherto-uncultured bacteria in crystallizer ponds (salinity, from 30 to 37%) from multipond solar salterns. in the present study, these bacteria constituted from 5 to 25% of the total prok ... | 2000 | 10877805 |
| biofilm community structure in polluted rivers: abundance of dominant phylogenetic groups over a complete annual cycle. | the seasonal dynamics of river biofilm communities in two german rivers, the elbe and one of its tributaries, the spittelwasser, were investigated for the first time by using fluorescence in situ hybridization and a standardized biofilm sampling procedure. we show the importance of members of the beta subclass of the class proteobacteria, which formed the largest single group in the massively polluted spittelwasser at all times. clear seasonal peaks of abundance were observed for the planctomyce ... | 2000 | 10877809 |
| identification of 16s ribosomal dna-defined bacterial populations at a shallow submarine hydrothermal vent near milos island (greece). | in a recent publication (s. m. sievert, t. brinkhoff, g. muyzer, w. ziebis, and j. kuever, appl. environ. microbiol. 65:3834-3842, 1999) we described spatiotemporal changes in the bacterial community structure at a shallow-water hydrothermal vent in the aegean sea near the isle of milos (greece). here we describe identification and phylogenetic analysis of the predominant bacterial populations at the vent site and their distribution at the vent site as determined by sequencing of dna molecules ( ... | 2000 | 10877814 |
| the natural evolutionary relationships among prokaryotes. | two contrasting and very different proposals have been put forward to account for the evolutionary relationships among prokaryotes. the currently widely accepted three domain proposal by woese et al. (proc. natl. acad. sci. usa (1990) 87: 4576-4579) calls for the division of prokaryotes into two primary groups or domains, termed archaebacteria (archaea) and eubacteria (bacteria), both of which are suggested to have originated independently from a universal ancestor. however, this proposal, which ... | 2000 | 10890353 |
| diversity of thiosulfate-oxidizing bacteria from marine sediments and hydrothermal vents. | species diversity, phylogenetic affiliations, and environmental occurrence patterns of thiosulfate-oxidizing marine bacteria were investigated by using new isolates from serially diluted continental slope and deep-sea abyssal plain sediments collected off the coast of new england and strains cultured previously from galapagos hydrothermal vent samples. the most frequently obtained new isolates, mostly from 10(3)- and 10(4)-fold dilutions of the continental slope sediment, oxidized thiosulfate to ... | 2000 | 10919760 |
| effect of field inoculation with sinorhizobium meliloti l33 on the composition of bacterial communities in rhizospheres of a target plant (medicago sativa) and a non-target plant (chenopodium album)-linking of 16s rrna gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria. | fourteen weeks after field release of luciferase gene-tagged sinorhizobium meliloti l33 in field plots seeded with medicago sativa, we found that the inoculant also occurred in bulk soil from noninoculated control plots. in rhizospheres of m. sativa plants, s. meliloti l33 could be detected in noninoculated plots 12 weeks after inoculation, indicating that growth in the rhizosphere preceded spread into bulk soil. to determine whether inoculation affected bacterial diversity, 1,119 bacteria were ... | 2000 | 10919821 |
| [screening of marine bacteria for fucoidan hydrolases]. | twenty-five strains of epiphytic marine bacteria isolated from the brown algae fucus evanescens and chorda filum and fifty-three bacteria isolated from the sea cucumber apostichopus japonicus were screened for fucoidanases using fucoidans prepared from the brown algae f. evanescens, laminaria cichorioides, and l. japonica. eighteen bacterial epiphytes and thirty-eight bacterial isolates from the sea cucumber were found to contain fucoidanases, which were able to hydrolyze either all of the fucoi ... | 2000 | 10920807 |
| phylogenetic analysis of bacterial communities in mesophilic and thermophilic bioreactors treating pharmaceutical wastewater. | the phylogenetic diversity of the bacterial communities supported by a seven-stage, full-scale biological wastewater treatment plant was studied. these reactors were operated at both mesophilic (28 to 32 degrees c) and thermophilic (50 to 58 degrees c) temperatures. community fingerprint analysis by denaturing gradient gel electrophoresis (dgge) of the pcr-amplified v3 region of the 16s rrna gene from the domain bacteria revealed that these seven reactors supported three distinct microbial commu ... | 2000 | 10966414 |
| the phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. | the evolutionary relationships of proteobacteria, which comprise the largest and phenotypically most diverse division among prokaryotes, are examined based on the analyses of available molecular sequence data. sequence alignments of different proteins have led to the identification of numerous conserved inserts and deletions (referred to as signature sequences), which either are unique characteristics of various proteobacterial species or are shared by only members from certain subdivisions of p ... | 2000 | 10978543 |
| phylogenetic characterization and in situ detection of a cytophaga-flexibacter-bacteroides phylogroup bacterium in tuber borchii vittad. ectomycorrhizal mycelium. | mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. in this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus tuber borchii vittad. universal eubacterial primers specific for the 5' and 3' ends of the 16s rrna gene (16s rdna) were used for pcr ampli ... | 2000 | 11055961 |
| comparative 16s rrna analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. | in a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16s ribosomal dna (rdna) sequences from three different lakes (lake gossenköllesee, austria; lake fuchskuhle, germany; and lake baikal, russia). the phylogenetic comparison with the currently available rdna data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rdna sequences of primarily freshwater and soil, but not marine, origin. six of t ... | 2000 | 11055963 |
| isolation and characterization of 23 carbofuran-degrading bacteria from soils from distant geographical areas. | the aim of this work was to isolate, identify and type carbofuran-degrading bacteria from two geographically distant soils. restriction fragment length polymorphism (rflp) patterns of the 16s rrna gene and partial 16s rrna sequence analysis were used to classify the 23 isolates obtained. nine of them showed high similarity to pseudomonas strains, seven showed similarity to the flexibacter/cytophaga/bacteroides group and the remainder showed similarity to other bacterial genera. isolates within t ... | 2000 | 11069636 |
| community composition of marine bacterioplankton determined by 16s rrna gene clone libraries and fluorescence in situ hybridization. | we determined the compositions of bacterioplankton communities in surface waters of coastal california using clone libraries of 16s rrna genes and fluorescence in situ hybridization (fish) in order to compare the community structures inferred from these two culture-independent approaches. the compositions of two clone libraries were quite similar to those of clone libraries of marine bacterioplankton examined by previous studies. clones from gamma-proteobacteria comprised ca. 28% of the librarie ... | 2000 | 11097877 |
| investigation of 0.2 µm filterable bacteria from the western mediterranean sea using a molecular approach: dominance of potential starvation forms. | although the existence of 0.2 µm filterable bacteria has been known since the early 80's, they are not taken into consideration when modeling microbial food webs, due to an overall lack of information concerning this specific size class. according to physiological studies on starvation forms and investigations on small bacterial cells in marine ecosystems, a 0.2 µm filtrate may consist of different phenotypes: starvation forms of typical marine bacteria, ultramicrobacteria or bacterial cells, ev ... | 2000 | 10640668 |
| cloning and characterization of the flavobacterium johnsoniae gliding-motility genes gldb and gldc. | the mechanism of bacterial gliding motility (active movement over surfaces without the aid of flagella) is not known. a large number of mutants of the gliding bacterium flavobacterium johnsoniae (cytophaga johnsonae) with defects in gliding motility have been previously isolated, and genetic techniques to analyze these mutants have recently been developed. we complemented a nongliding mutant of f. johnsoniae (uw102-99) with a library of wild-type dna by using the shuttle cosmid pcp26. the comple ... | 2000 | 10648514 |
| identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis. | the microbial assemblages of lake cisó and lake vilar (banyoles, northeast spain) were analyzed in space and time by microscopy and by performing pcr-denaturing gradient gel electrophoresis (dgge) and sequence analysis of 16s rrna gene fragments. samples obtained from different water depths and at two different times of the year (in the winter during holomixis and in the early spring during a phytoplankton bloom) were analyzed. although the lakes have the same climatic conditions and the same wa ... | 2000 | 10653710 |
| 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 ge ... | 2000 | 10698791 |
| description of cellulophaga algicola sp. nov., isolated from the surfaces of antarctic algae, and reclassification of cytophaga uliginosa (zobell and upham 1944) reichenbach 1989 as cellulophaga uliginosa comb. nov. | a group of strains with potent extracellular enzymic activity were isolated from the surfaces of the chain-forming sea-ice diatom melosira and from an unidentified macrophyte collected from the eastern antarctic coastal zone. 16s rdna sequence analysis indicated that the strains belonged to the genus cellulophaga and showed greatest similarity to the species cellulophaga baltica (sequence similarity 97%). phenotypic characteristics, dna base composition and dna-dna hybridization values clearly s ... | 2000 | 11034497 |
| characterization of the microbial community of lotic organic aggregates ('river snow') in the elbe river of germany by cultivation and molecular methods. | aerobic and anaerobic cultivation techniques, 16s rdna-based phylogeny, and fluorescent in situ hybridization were used to describe the phylogenetic diversity and physiological versatility of lotic microbial aggregates ('river snow') obtained from the river elbe. in the course of the year the 'river snow' community changed. it was characterized by a great bacterial diversity in spring, the predominant occurrence of algae in summer and reduction of the total bacterial cell count in autumn and win ... | 2000 | 10967215 |
| microflora of technogenous wastes characterised by fatty acid profiling. | fatty acid methyl ester (fame) profiles obtained directly in situ have been used to estimate microbial community structure in different technogenous wastes. the effect of nutrients added, simulating the effect of plant-derived exudates on the indigenous microflora in the heaps during the reclamation process, was also studied in microcosms. the wastes such as coal-mine spoil, non-ferrous metallurgical slag and coal fly-ash were characterised by a poorly developed microflora as compared to a typic ... | 2000 | 11061183 |
| unravelling the genetic diversity of ruminal bacteria belonging to the cfb phylum. | molecular biology approaches were employed to examine the genetic diversity of bacteria from the cytophaga/flexibacter/bacteroides (cfb) phylum in the rumen of cattle. by this means we were able to identify cultured strains that represent some of the larger cfb clusters previously identified only by pcr amplification and sequencing. complete 16s rdna sequences were obtained for 16 previously isolated rumen strains, including the type strains of prevotella ruminicola, p. bryantii, p. brevis and p ... | 2000 | 10922505 |
| molecular analysis of microbial communities in mobile deltaic muds of southeastern papua new guinea. | a culture-independent examination of microbial diversity in mobile deltaic sediments from the gulf of papua, papua new guinea, was conducted by sequence analysis of 16s rdna clone library. universal small subunit primers were used to amplify dna extracted from the sediment. of 91 clones randomly selected from the library, 33 contained unique non-chimeric sequences. analysis of these unique sequences showed that the majority of them belonged to bacteria (94.5%), with proteobacteria being the domi ... | 2000 | 10967214 |
| taxonomy of antarctic flavobacterium species: description of flavobacterium gillisiae sp. nov., flavobacterium tegetincola sp. nov., and flavobacterium xanthum sp. nov., nom. rev. and reclassification of [flavobacterium] salegens as salegentibacter salegens gen. nov., comb. nov. | 16s rrna phylogenetic analysis of a number of yellow- and orange-pigmented strains isolated from a variety of antarctic habitats including sea ice, lakewater and cyanobacterial mats indicated a close relationship to the genus flavobacterium but distinct from known flavobacterium species. phenotypic properties, dna g+c content and whole-cell fatty acid profiles of the antarctic strains were consistent with those of the genus flavobacterium. dna-dna hybridization analysis indicated the presence of ... | 2000 | 10843045 |
| increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input. | despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. in this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16s rdna sequences. the similarity coefficients of restriction fragment len ... | 2000 | 10698758 |
| changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques. | dilution cultures are a common technique for measuring the growth of bacterioplankton communities. in this study, the taxonomic composition of marine bacterioplankton dilution cultures was followed in water samples from plymouth sound and the english channel (uk). bacterial abundances as well as protein and dna content were closely monitored by flow cytometry. denaturing gradient gel electrophoresis (dgge) of polymerase chain reaction (pcr)-amplified 16s rdna fragments and fluorescence in situ h ... | 2000 | 11220305 |
| [clusterization of halophilic and halotolerant eubacteria using whole-cell protein electrophoresis data]. | total cell proteins of the nineteen halophilic and halotolerant eubacteria isolated from marine sediments and highly mineralized formation waters of oil fields were investigated by sds gel electrophoresis. the microorganisms studied, phenotypically identified as belonging to the genera dietzia, rhodococcus, staphylococcus, cytophaga, brevibacterium, and archangium, were found to form clearly distinguishable clusters (20-30% similarity at the generic level) on the dendrogram derived from electrop ... | 2000 | 11315673 |
| news & notes: detection of microorganisms with overall cellulolytic activity. | a modification is described of the plate method for the detection of microorganisms with overall cellulolytic activity, including those like cytophaga, in which the activity is cell bound. within a few days of incubation colonies of cellulose-degrading bacteria formed holes in discs of lens paper placed on freshly inoculated agar plates. | 2000 | 10594230 |
| 16s rrna-targeted oligonucleotide probes for the in situ detection of members of the phylum cytophaga-flavobacterium-bacteroides. | bacteria of the cytophaga-flavobacterium-bacteroides phylum (cfb-phylum) are numerically important members of many microbial communities. a suite of five 16s rrna-targeted oligonucleotide probes for members of this group is described which was designed to dominantly target bacteria of the cfb-phylum that are found in particular habitats. for this we initially performed a literature survey-for the sources and sites of isolation of hitherto described members of the cfb-phylum. probe cfb286 is most ... | 2000 | 10879984 |
| muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from german north sea intertidal sediment. | a gram-negative, facultatively anaerobic bacterium with appendages was isolated from continuous cultures with a seawater-sediment suspension containing hexadecane as the sole carbon source. although this organism was isolated from a hexadecane-degrading bacterial community, it was not able to degrade hexadecane. however, this bacterium was able to use different sugars and amino acids for growth, indicating that it probably profits from the lysis or from products like surfactants of other cells i ... | 2001 | 11760940 |
| isolation of novel pelagic bacteria from the german bight and their seasonal contributions to surface picoplankton. | we tested new strategies for the isolation of abundant bacteria from coastal north sea surface waters, which included reducing by several orders of magnitude the concentrations of inorganic n and p compounds in a synthetic seawater medium. agar plates were resampled over 37 days, and slowly growing colonies were allowed to develop by repeatedly removing all newly formed colonies. a fivefold increase of colonies was observed on plates with reduced nutrient levels, and the phylogenetic composition ... | 2001 | 11679337 |
| phylogenetic analysis and taxonomic study of marine cytophaga-like bacteria: proposal for tenacibaculum gen. nov. with tenacibaculum maritimum comb. nov. and tenacibaculum ovolyticum comb. nov., and description of tenacibaculum mesophilum sp. nov. and tenacibaculum amylolyticum sp. nov. | bacterial strains were isolated from sponge and green algae which were collected on the coast of japan and palau. the phylogenetic relationships of these isolates among marine species of the cytophaga-flavobacterium-bacteroides complex were analysed by using their gyrb nucleotide sequences and translated peptide sequences (gyrb) in addition to 16s rdna sequences. these isolates were closely related to the previously characterized marine flexibacter species, [flexibacter] maritimus and [flexibact ... | 2001 | 11594591 |
| changes in the epilimnetic bacterial community composition, production, and protist-induced mortality along the longitudinal axis of a highly eutrophic reservoir. | we studied changes in the epilimnetic bacterial community composition (bcc), bacterial biomass and production, and protistan succession and bacterivory along the longitudinal axis of the canyon-shaped, highly eutrophic sau reservoir (ne spain) during two sampling campaigns, in april and july 1997. longitudinal changes in bcc from the river inflow to the dam area of the reservoir were detected by using oligonucleotide probes targeted to the kingdom bacteria, to the alpha, beta, and gamma subclass ... | 2001 | 12024261 |
| phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (brassica napus cv. westar) employing cultivation-dependent and cultivation-independent approaches. | the structure of the microbial rhizoplane community of the important crop plant oilseed rape was studied by using a culture-dependent as well as a culture-independent approach based on 16s rdna amplification. after isolation of the microbial community from the rhizoplane of oilseed rape (brassica napus cv. westar), the collected suspension was divided into two parts. one part was used for cultivation of bacteria onto three different growth media to establish a culture collection. from the other ... | 2001 | 12024277 |
| 2-bromoethanesulfonate affects bacteria in a trichloroethene-dechlorinating culture. | long-term exposure to 2-bromoethanesulfonate (bes), an agent known to inhibit methanogenesis, altered the bacterial community structure of an anaerobic enrichment culture that reductively dechlorinated trichloroethene (tce). bes did not hinder the dechlorination of tce or other chlorinated ethenes as previously reported, although different intermediates and end products were observed. | 2001 | 11319126 |
| in situ identification of polyphosphate- and polyhydroxyalkanoate-accumulating traits for microbial populations in a biological phosphorus removal process. | polyphosphate- and polyhydroxyalkanoate (pha)-accumulating traits of predominant microorganisms in an efficient enhanced biological phosphorus removal (ebpr) process were investigated systematically using a suite of non-culture-dependent methods. results of 16s rdna clone library and fluorescence in situ hybridization (fish) with rrna-targeted, group-specific oligonucleotide probes indicated that the microbial community consisted mostly of the alpha- (9.5% of total cells), beta- (41.3%) and gamm ... | 2001 | 11321541 |
| molecular detection of marine bacterial populations on beaches contaminated by the nakhodka tanker oil-spill accident. | in january 1997, the tanker nakhodka sank in the japan sea, and more than 5000 tons of heavy oil leaked. the released oil contaminated more than 500 km of the coastline, and some still remained even by june 1999. to investigate the long-term influence of the nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturi ... | 2001 | 11359510 |
| changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir. | bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce (<0.8-microm treatment) or enhance (<5-microm treatment) protistan grazing and then incubated in situ for 96 h in dialysis bags. time course samples were taken from the bags and the reservoir to estimate bacterial abundance, mean cell volume, production, protistan grazing, viral abundance, and frequency of visibly infected cells. shifts in bacterial community composition (bcc) were examined by denaturing gradien ... | 2001 | 11375187 |
| study of microbial community of brewery-treating granular sludge by denaturing gradient gel electrophoresis of 16s rrna gene. | the microbial community structure of granular sludge from an upflow anaerobic sludge blanket (uasb) reactor treating brewery effluent was studied by denaturing gradient gel electrophoresis (dgge). twelve major bands were observed in the dgge fingerprint for the bacteria domain and four bands for the archaea domain. of the bacterial bands observed, six were successfully purified and sequenced. among them, three were related to the gram-positive low g + c group, one to the delta subclass of the pr ... | 2001 | 11379115 |
| 16s rrna in situ probing for the determination of the family level community structure implicated in enhanced biological nutrient removal. | knowledge of a discrete physiological group capable of excess biological phosphate removal (ebpr) remains unclear. consequently, microbial community analysis of an enhanced continuous laboratory-scale activated sludge process displaying a strong ebpr mechanism was conducted. unit design was configured upon the three-stage phoredox process and characterization of the activated sludge bacterial community was carried out using fluorescent in situ hybridization (fish) techniques. fixed activated slu ... | 2001 | 11379117 |
| in situ polychlorophenol bioremediation potential of the indigenous bacterial community of boreal groundwater. | the composition and chlorophenol-degrading potential of groundwater bacterial community in a permanently cold, oxygen-deficient chlorophenol contaminated aquifer at kärkölä, finland was studied with the aim of evaluating in situ bioremediation potential. the groundwater contained from 10(4) to 10(7) microscopically counted cells/ml and up to 10(5) cfu/ml heterotrophic bacteria cultivable at 8 and 20 degrees c. of the 102 pure cultures, of which 86% gram-negative, from the plume area (10,000 micr ... | 2001 | 11394785 |
| characterization of facultative oligotrophic bacteria from polar seas by analysis of their fatty acids and 16s rdna sequences. | one hundred and seventy three bacterial strains, isolated previously after enrichment under oligotrophic, psychrophylic conditions from arctic (98 strains) and antarctic seawater (75 strains), were characterized by gas-liquid chromatographic analysis of their fatty acid compositions. by numerical analysis, 8 clusters, containing 2 to 59 strains, could be delineated, and 8 strains formed separate branches. five clusters contained strains from both poles, two minor clusters were confined to arctic ... | 2001 | 11403404 |
| zobellia galactanovorans gen. nov., sp. nov., a marine species of flavobacteriaceae isolated from a red alga, and classification of [cytophaga] uliginosa (zobell and upham 1944) reichenbach 1989 as zobellia uliginosa gen. nov., comb. nov. | a mesophilic, aerobic, non-flagellated, gliding bacterium, forming yellow colonies and designated dsijt, was isolated from a red alga on the sea-shore of roscoff, brittany, france. dsijt was selected for its ability to actively degrade both agars and carrageenans. the gram-negative cells occurred singly or in pairs as long rods. the temperature range for growth was 13-45 degrees c, with an optimum at 35 degrees c. the ph range for growth at 35 degrees c was from 6.0 to 8.5, with an optimum aroun ... | 2001 | 11411725 |
| microbial populations associated with treatment of an industrial dye effluent in an anaerobic baffled reactor. | fluorescent in situ hybridization (fish) using 16s and 23s rrna-targeted probes together with construction of an archaeal 16s ribosomal dna (rdna) clone library was used to characterize the microbial populations of an anaerobic baffled reactor successfully treating industrial dye waste. wastewater produced during the manufacture of food dyes containing several different azo and other dye compounds was decolorized and degraded under sulfidogenic and methanogenic conditions. use of molecular metho ... | 2001 | 11425746 |
| the contribution of halophilic bacteria to the red coloration of saltern crystallizer ponds(1). | analysis of the pigments extracted from solar saltern crystallizer ponds in santa pola near alicante and on the balearic island of mallorca, spain, showed that 5-7.5% of the total prokaryotic pigment absorbance could be attributed to a novel carotenoid or carotenoid-like compound. this unidentified pigment was identical to the sole pigment present in salinibacter ruber, the only described member of a newly discovered genus of red halophilic bacteria related to the cytophaga-flavobacterium-bacter ... | 2001 | 11451516 |
| multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton. | the diversity of cultured planktonic bacteria was analyzed. bacterial strains were isolated from a eutrophic lake (zwischenahner meer, niedersachsen, germany) at three different sampling dates (october 1997, april and may 1998). phylogenetic diversity was assessed by polymerase chain reaction (pcr), denaturing gradient gel electrophoresis (dgge), and sequencing of 16s rrna gene fragments. enterobacterial repetitive intergenic consensus (eric)-pcr revealed a high genomic diversity within the stra ... | 2001 | 11451519 |