| 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 |
| 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 |
| 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 |
| 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 |
| [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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| quantitative molecular analysis of the microbial community in marine arctic sediments (svalbard). | fluorescence in situ hybridization (fish) and rrna slot blot hybridization with 16s rrna-targeted oligonucleotide probes were used to investigate the phylogenetic composition of a marine arctic sediment (svalbard). fish resulted in the detection of a large fraction of microbes living in the top 5 cm of the sediment. up to 65.4% +/- 7.5% of total dapi (4',6'-diamidino-2-phenylindole) cell counts hybridized to the bacterial probe eub338, and up to 4.9% +/- 1.5% hybridized to the archaeal probe arc ... | 2001 | 11133470 |
| phylogenetic diversity of bacteria associated with the marine sponge rhopaloeides odorabile. | molecular techniques were employed to document the microbial diversity associated with the marine sponge rhopaloeides odorabile. the phylogenetic affiliation of sponge-associated bacteria was assessed by 16s rrna sequencing of cloned dna fragments. fluorescence in situ hybridization (fish) was used to confirm the presence of the predominant groups indicated by 16s rdna analysis. the community structure was extremely diverse with representatives of the actinobacteria, low-g+c gram-positive bacter ... | 2001 | 11133476 |
| microbial community dynamics in mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. | a mesocosm experiment was performed to study the influence of nutrients on activity and diversity of bacterial assemblages from the mediterranean sea. changes in the diversity of the predominant bacterial populations were monitored by dgge fingerprinting of pcr products derived from 16s rrna encoding genes. fluctuations in the diversity of the most active populations was inferred by performing the dgge fingerprinting on the basis of the cellular rrna after reverse transcription and pcr amplifica ... | 2001 | 11137604 |
| microbial community dynamics in mediterranean nutrient-enriched seawater mesocosms: changes in abundances, activity and composition. | quantitative and qualitative changes in bacterial communities from the mediterranean sea were compared in duplicate batch mesocosms with or without addition of inorganic nutrients. methods including traditional microbial ecology techniques, molecular biology and flow cytometry were combined to determine abundances, production, cell size, activity, culturability and taxonomic diversity of bacterial cells. addition of nutrients and confinement resulted in an increase of bacterial densities which w ... | 2001 | 11137605 |
| alpha- and beta-proteobacteria control the consumption and release of amino acids on lake snow aggregates. | we analyzed the composition of aggregate (lake snow)-associated bacterial communities in lake constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rrna-targeted oligonucleotide probes of various specificity. in addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. generally, between 40 and m ... | 2001 | 11157226 |
| impact of uv radiation on bacterioplankton community composition. | the potential effect of uv radiation on the composition of coastal marine bacterioplankton communities was investigated. dilution cultures with seawater collected from the surface mixed layer of the coastal north sea were exposed to different ranges of natural or artificial solar radiation for up to two diurnal cycles. the composition of the bacterioplankton community prior to exposure was compared to that after exposure to the different radiation regimes using denaturing gradient gel electropho ... | 2001 | 11157229 |
| phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. | we used in situ hybridization with fluorescently labeled rrna-targeted oligonucleotide probes concurrently with measurements of bacterial carbon production, biomass, and extracellular polymeric substances (eps) to describe the bacterial community in sediments along a glacial stream. the abundance of sediment-associated archaea, as detected with the arch915 probe, decreased downstream of the glacier snout, and a major storm increased their relative abundance by a factor of 5.5 to 7.9. bacteria of ... | 2001 | 11157246 |
| pcr primers and functional probes for amplification and detection of bacterial genes for extracellular peptidases in single strains and in soil. | a set of primers and functional probes was developed for the detection of peptidase gene fragments of proteolytic bacteria. based on dna sequence data, degenerate pcr primers and internal dig-labeled probes specific for genes encoding alkaline metallopeptidases (apr) (e.3.4.24), neutral metallopeptidases (npr) (e.3.4.24) and serine peptidases (sub) (e.3.4.21) were derived by multiple sequence alignments. type strains with known peptidase genes and proteolytic bacteria from a grassland rhizospher ... | 2001 | 11165346 |
| 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 |
| 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 |
| bacterial populations colonizing and degrading rice straw in anoxic paddy soil. | rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. the bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. rice straw was incubated in paddy soil anaerobically for 71 days. denaturing gradient gel electrophoresis (dgge) of the amplified bacterial 16s rrna genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incub ... | 2001 | 11229927 |
| phylogenetic analysis of the succession of bacterial communities in the great south bay (long island). | bacterial community composition and succession were examined over the course of the summer season in the great south bay, long island, ny, usa, using a 16s rdna clone library approach. there was a progression of changes in dominant species in the libraries during the summer of 1997. the july library had several groups dominant, the sar407 relatives of the alpha-proteobacteria (24%) and the sar86 (18%), sulfur-oxidizing symbiont relatives (8%) of the gamma-proteobacteria, and unidentified cytopha ... | 2001 | 11248393 |
| phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the cariaco basin. | microbial community samples were collected from the anoxic zone of the cariaco basin at depths of 320, 500, and 1,310 m on a november 1996 cruise and were used to construct 16s ribosomal dna libraries. of 60 nonchimeric sequences in the 320-m library, 56 belonged to the epsilon subdivision of the proteobacteria (epsilon-proteobacteria) and 53 were closely related to ectosymbionts of rimicaris exoculata and alvinella pompejana, which are referred to here as epsilon symbiont relatives (esr). the 5 ... | 2001 | 11282619 |
| 16s rdna diversity of cultured and uncultured prokaryotes of a mat sample from lake fryxell, mcmurdo dry valleys, antarctica. | the prokaryotic diversity of aerobic and anaerobic bacterial isolates and of bacterial and archaeal 16s rdna clones was determined for a microbial mat sample from the moated region of lake fryxell, mcmurdo dry valleys, antarctica. among the anaerobic bacteria, members of clostridium estertheticum and some other psychrotolerant strains dominated whereas methanogens and other archaea were lacking. isolates highly related to flavobacterium hibernum, janthiniobacterium lividum, and arthrobacter flav ... | 2001 | 11302499 |
| the microbial diversity in picoplankton enrichment cultures: a molecular screening of marine isolates. | picoplankton bacteria from a north sea water sample were cultured under a variety of different conditions (nutrients, temperature, light, agitation, adhesion). fluorescent in situ hybridization (fish) analysis of the enrichments showed complex communities which were dominated by gamma-proteobacteria or beta-proteobacteria, followed by alpha-proteobacteria and bacteria from the cytophaga/flavobacterium/bacteroides (cfb) cluster. among 410 isolates, a high degree of diversity was found, both with ... | 2001 | 11311435 |
| a molecular phylogenetic survey of sea-ice microbial communities (simco). | 16s rdna clone library analysis was used to identify bacterial biodiversity in a variety of sea-ice microbial communities (simco). dna was extracted from seven antarctic sea-ice samples and one arctic sea-ice sample and 16s rdna pcr-amplified using universal and archaea-specific primers. recombinant 16s rdna clones were obtained and dereplicated using restriction fragment length polymorphism analysis (rflp). after rflp analysis, 100 distinct phylotypes (a unique clone or group of clones with seq ... | 2001 | 11311437 |
| [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 |
| 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 |
| clogging of a limestone fracture by stimulating groundwater microbes. | biological clogging is promoted in aquifers either to contain or to remediate groundwater. in this study, an apparatus able to detect small changes in hydraulic conductivity (k) was developed to measure the clogging of a single fracture in limestone, following microbial stimulation. the fracture had a 2.5 mm2 section and was 50 cm long. prior to the inoculation of the limestone, the sequencing of representative clones from 16s rrna genes isolated from groundwater, showed significant affiliation ... | 2001 | 11337851 |
| phylogenetic analyses of caulerpa taxifolia (chlorophyta) and of its associated bacterial microflora provide clues to the origin of the mediterranean introduction. | the accidental introduction of caulerpa taxifolia into the mediterranean is no longer under dispute. what has eluded researchers until now, is definitive evidence for the original, biogeographical source population. here we present two independent lines of evidence that support an australian origin for the mediterranean populations of c. taxifolia. first, we reanalysed algal rdna-internal transcribed spacer (rdna-its) sequences, combining previously published sequences from different studies wit ... | 2001 | 11348502 |
| 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 |
| growth of chitinolytic dune soil beta-subclass proteobacteria in response to invading fungal hyphae. | it has frequently been reported that chitinolytic soil bacteria, in particular biocontrol strains, can lyse living fungal hyphae, thereby releasing potential growth substrate. however, the conditions used in such assays (high bacterial density, rich media, fragmented hyphae) make it difficult to determine whether mycolytic activity is actually of importance for the growth and survival of chitinolytic bacteria in soils. an unidentified group of beta-subclass proteobacteria (cbetaps) was most domi ... | 2001 | 11472904 |
| flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from antarctica. | a psychrophilic, aerobic bacterium designated a2it was isolated from marine sediment recovered from shallow waters surrounding adelaide island, antarctica (67 degrees 34' s, 68 degrees 07' w). the organism exhibited xylanolytic and laminarinolytic activity and was halotolerant. basic characterization showed that it was gram-negative, non-motile, yellow-pigmented (beta,beta-carotene-3,3'-diol) and positive for oxidase and catalase synthesis. analysis of the 16s rdna sequence suggests that the org ... | 2001 | 11491319 |
| polyamine distribution profiles in the eighteen genera phylogenetically located within the flavobacterium-flexibacter-cytophaga complex. | cellular polyamines of eighteen genera belonging to the flavobacterium-flexibacter-cytophaga complex were analysed by ion exchange liquid chromatography. homospermidine was the major polyamine in the genera bergeyella, riemerella, ornithobacterium, weeksella, capnocytophaga, polaribacter and psychroflexus belonging to the family flavobacteriaceae. in the family spirosomaceae, runella, spirosoma and flectobacillus species contained spermidine whereas cyclobacterium species contained homospermidin ... | 2001 | 11491527 |
| systematics and evolution of ruminal species of the genus prevotella. | bacterial species of the genus prevotella represent a numerically dominant microbial population in the rumen of cattle. they belong to the phylogenetic division cytophaga-flexibacter-bacteroides (cfb) which is a large group of ecologically diverse bacteria with only a few shared traits. the phylogenetic descent from a common ancestor seems to be unquestionable, however, as judged from the small subunit ribosomal rna analysis. only 4 ruminal prevotella species have been described to date, even th ... | 2001 | 11501474 |
| psychrophilic valine dehydrogenase of the antarctic psychrophile, cytophaga sp. kuc-1: purification, molecular characterization and expression. | we found the occurrence of valine dehydrogenase in the cell extract of a psychrophilic bacterium, cytophaga sp. kuc-1, isolated from antarctic seawater and purified the enzyme to homogeneity. the molecular mass of the enzyme was determined to be approximately 154 kda by gel filtration and that of the subunit was 43 kda by sds/page: the enzyme was a homotetramer. the enzyme required nad+ as a coenzyme, and catalyzed the oxidative deamination of l-valine, l-isoleucine, l-leucine and the reductive ... | 2001 | 11502197 |
| molecular identification of microorganisms from endodontic infections. | a relatively wide range of bacteria have been isolated from root canals using standard culture techniques. however, only 50% of the bacteria in the oral cavity are cultivable (s. s. socransky et al., arch. oral biol. 8:278-280, 1963); hence, bacterial diversity in endodontic infections is underestimated. this study used a pcr-based 16s rrna gene assay, followed by cloning and sequencing of 16s rrna amplicons from a small subset of samples to assess the diversity of bacteria present in infected r ... | 2001 | 11526164 |
| the use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that fibrobacter diverged at a similar time to chlamydia and the cytophaga-flavobacterium-bacteroides division. | the phylogenetic placement of the rumen bacterium fibrobacter succinogenes was determined using a signature sequence approach that allows determination of the relative branching order of the major divisions among bacteria [gupta, r. s. (2000) fems microbiol rev 24, 367-402]. for this purpose, segments of the hsp60 (groel), hsp70 (dnak), ctp synthase and alanyl-trna synthetase genes, which are known to contain signature sequences that are useful for phylogenetic deterministic purposes, were clone ... | 2001 | 11535801 |
| a partial phylogenetic analysis of the "flavobacter-bacteroides" phylum: basis for taxonomic restructuring. | on the basis of small subunit rrna sequence analyses five major subgroups within the flavobacteria-bacteroides phylum have been defined. these are tentatively designated the cytophaga subgroup (comprising largely cytophaga species), the flavobacter subgroup (comprising the true flavobacteria and the polyphyletic genus weeksella), the bacteroides subgroup (comprising the bacteroides and certain cytophaga-like bacteria), the sphingobacter subgroup (which contains the known sphingolipid-producing m ... | 1992 | 11541229 |
| 5s ribosomal ribonucleic acid sequences in bacteroides and fusobacterium: evolutionary relationships within these genera and among eubacteria in general. | the 5s ribosomal ribonucleic acid (rrna) sequences were determined for bacteroides fragilis, bacteroides thetaiotaomicron, bacteroides capillosus, bacteroides veroralis, porphyromonas gingivalis, anaerorhabdus furcosus, fusobacterium nucleatum, fusobacterium mortiferum, and fusobacterium varium. a dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5s rrna sequences, showed differences as well as similarities with ... | 1989 | 11542181 |
| bacterial gliding motility: multiple mechanisms for cell movement over surfaces. | the mechanisms responsible for bacterial gliding motility have been a mystery for almost 200 years. gliding bacteria move actively over surfaces by a process that does not involve flagella. gliding bacteria are phylogenetically diverse and are abundant in many environments. recent results indicate that more than one mechanism is needed to explain all forms of bacterial gliding motility. myxococcus xanthus "social gliding motility" and synechocystis gliding are similar to bacterial "twitching mot ... | 2001 | 11544349 |
| comparative genomics and evolution of genes encoding bacterial (p)ppgpp synthetases/hydrolases (the rel, rela and spot proteins). | in the gram-negative model organism escherichia coli, the effector molecule of the stringent response, (p)ppgpp, is synthesized by two different enzymes, rela and spot, whereas in the gram-positive model organism bacillus subtilis only one enzyme named rel is responsible for this activity. rel and spot also possess (p)ppgpp hydrolase activity. blast searches were used to identify orthologous genes in databases. the construction and bootstrapping of phylogenetic trees allowed classification of th ... | 2001 | 11545276 |
| polyamine distribution profiles in newly validated genera and species within the flavobacterium-flexibacter-cytophaga-sphingobacterium complex. | cellular polyamines of 58 strains belonging to the flavobacterium-flexibacter-cytophaga-sphingobacterium complex were analysed by hplc. homospermidine was found in all species of flavobacterium, chryseobacterium, empedobacter, myroides, cellulophaga, salegentibacter, psychroserpens and gelidibacter of the family flavobacteriaceae. flavobacterium ferrugineum located outside of this family also contained homospermidine. cytophaga fermentans and c. xylanolytica belonging to the family bacteroidacea ... | 2001 | 11548199 |
| members of the cytophaga-flavobacterium-bacteroides phylum as intracellular bacteria of acanthamoebae: proposal of 'candidatus amoebophilus asiaticus'. | three gram-negative, rod-shaped bacteria that were found intracellularly in two environmental and one clinical acanthamoeba sp. isolates were analysed. two endocytobionts showing a parasitic behaviour were propagated successfully outside their amoebal host cells and were identified subsequently by comparative 16s rrna sequence analysis as being most closely affiliated with flavobacterium succinicans (99% 16s rrna sequence similarity) or flavobacterium johnsoniae (98% 16s rrna sequence similarity ... | 2001 | 11553234 |
| adhesion of the fish pathogen flavobacterium psychrophilum to unfertilized eggs of rainbow trout (oncorhynchus mykiss) and n-hexadecane. | the ability of flavobacterium psychrophilum, the causative agent of rainbow trout fry syndrome (rtfs) in fish, to attach to unfertilized rainbow trout (oncorhynchus mykiss) eggs and to hydrocarbon n-hexadecane was examined in the present study. | 2001 | 11555199 |
| a newly discovered bacterium associated with parthenogenesis and a change in host selection behavior in parasitoid wasps. | the symbiotic bacterium wolbachia pipientis has been considered unique in its ability to cause multiple reproductive anomalies in its arthropod hosts. here we report that an undescribed bacterium is vertically transmitted and associated with thelytokous parthenogenetic reproduction in encarsia, a genus of parasitoid wasps. although wolbachia was found in only one of seven parthenogenetic encarsia populations examined, the "encarsia bacterium" (eb) was found in the other six. among seven sexually ... | 2001 | 11592990 |
| 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 |
| effect of sampling method on the representative recovery of microorganisms from the surfaces of aquacultured finfish. | the objective of this study was to determine if a gentle rinse procedure was equivalent to the combination of excision and homogenization with a stomacher for the relative removal of various microorganisms from finfish fillets. fillets of hybrid striped bass and rainbow trout were obtained from local markets and sampled using three methods: rinse (r), excision followed by homogenization in a stomacher (s), and homogenization of fillets following a rinse (rs). microorganisms were enumerated on se ... | 2001 | 11601699 |
| 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 |
| comparison of cellular and biomass specific activities of dominant bacterioplankton groups in stratified waters of the celtic sea. | a flow-sorting technique was developed to determine unperturbed metabolic activities of phylogenetically characterized bacterioplankton groups with incorporation rates of [(35)s]methionine tracer. according to fluorescence in situ hybridization with rrna targeted oligonucleotide probes, a clade of alpha-proteobacteria, related to roseobacter spp., and a cytophaga-flavobacterium cluster dominated the different groups. cytometric characterization revealed both these groups to have high dna (hna) c ... | 2001 | 11679347 |
| isolation of bacteria and 16s rdnas from lake vostok accretion ice. | lake vostok, the largest subglacial lake in antarctica, is separated from the surface by approximately 4 km of glacial ice. it has been isolated from direct surface input for at least 420 000 years, and the possibility of a novel environment and ecosystem therefore exists. lake vostok water has not been sampled, but an ice core has been recovered that extends into the ice accreted below glacial ice by freezing of lake vostok water. here, we report the recovery of bacterial isolates belonging to ... | 2001 | 11683867 |
| biodegradation of methyl tert-butyl ether under various substrate conditions. | five aerobic enrichments efficient at degrading methyl tert-butyl ether (mtbe) under different substrate conditions were developed in well-mixed reactors containing a polyethlene porous pot for biomass retention. the five substrate conditions were as follows: mtbe alone; mtbe and diethyl ether (dee); mtbe and diisopropyl ether (dipe); mtbe and ethanol (etoh); and mtbe with benzene, toluene, ethylbenzene, and xylene (btex). all five cultures demonstrated greater than 99.9% removal of mtbe. additi ... | 2001 | 11718336 |
| automated image analysis and in situ hybridization as tools to study bacterial populations in food resources, gut and cast of lumbricus terrestris l. | an image analysis procedure was developed for bacterial cells after staining with the dna-intercalating dye 4'-6-diamidino-2-phenylindole (dapi), and after in situ hybridization with cy3-labeled, rrna-targeted oligonucleotide probes. dapi- and cy3-images were captured separately from the same scenery with a cooled digital video camera with three ccd chips for the basic colors red (r), green (g) and blue (b). using the appropriate filter sets, images of dapi-stained cells were captured with the r ... | 2002 | 11733082 |
| 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 |
| new degenerate cytophaga-flexibacter-bacteroides-specific 16s ribosomal dna-targeted oligonucleotide probes reveal high bacterial diversity in river taff epilithon. | river microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. in this study the bacterial diversity of river taff epilithon in south wales was investigated. a 16s ribosomal dna (rdna) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. the epilithon was found to be very diverse, with an estimated 59.6% of the bacteri ... | 2002 | 11772628 |
| phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the northern baltic sea. | the objective of our study was to isolate and determine the phylogenetic affiliation of culturable estuarine bacteria capable of catabolizing riverine dissolved organic matter (rdom) under laboratory conditions. additions of rdom consistently promoted the growth of estuarine bacteria in carbon-limited dilution cultures, with seasonal variation in growth rates and yields. at least 42 different taxa were culturable on solid agar media and, according to quantitative dna-dna hybridizations, constitu ... | 2002 | 11772648 |
| [isolation and characterization of cytophaga lytica lipopolysaccharide]. | lipopolysaccharide (lps) and its structural components: lipid a, o-specific polysaccharide (o-ps) and oligosaccharide core (og-core) have been isolated from cytophaga lytica. 3-oxytetradecanoic (40.8%) and dodecanoic (28.7%) are the predominant fatty acids of lipid a; pentadecanoic (6.8%), 3-oxyhexadecanoic (6.5%) as well as hexadecanoic (5.4%) acids have been found as well. the content of the rest of fatty acids is inconsiderable (2.3 to 0.5%). og-core contained monosaccharides both typical of ... | 2001 | 11785415 |
| phylogenetic composition of bacterioplankton assemblages from the arctic ocean. | we analyzed the phylogenetic composition of bacterioplankton assemblages in 11 arctic ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16s rrna genes. the sequencing effort was directed by denaturing gradient gel electrophoresis (dgge) screening of samples and the clone libraries. sequences of 88 clones fell into seven major lineages of the domain bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-p ... | 2002 | 11823184 |
| on the stability properties of a stochastic model for phage-bacteria interaction in open marine environment. | in this paper we extend the deterministic model for the epidemics induced by virulent phages on bacteria in marine environment introduced by beretta and kuang [math. biosci. 149 (1998) 57], allowing random fluctuations around the positive equilibrium. the stochastic stability properties of the model are investigated both analytically and numerically suggesting that the deterministic model is robust with respect to stochastic perturbations. | 2002 | 11825593 |
| anaerophaga thermohalophila gen. nov., sp. nov., a moderately thermohalophilic, strictly anaerobic fermentative bacterium. | the strictly anaerobic gram-negative bacterium strain fru22t grows at 50 degrees c in media containing up to 75 g nacl l(-1). hexoses and pentoses are fermented to equal molar amounts of acetate, propionate and succinate, and no co2 is formed. an orange-red pigment similar to flexirrubin is produced during stationary phase upon exposure to light for several days. cells also produce a surface-active extracellular compound which lowers the surface tension of the medium. this tenside is heat-tolera ... | 2002 | 11837300 |
| diverse bacteria related to the bacteroides subgroup of the cfb phylum within the gut symbiotic communities of various termites. | phylogenetically diverse clones of the partial 16s rdna (ca. 850 bp) of bacteria belonging to the bacteroides subgroup of the cytophaga-flavobacter-bacteroides phylum were collected from the symbiotic microbial communities in the guts of six termite species without cultivation. combined with the sequences reported previously, a total of thirty phylotypes of the subgroup were identified and classified into five phylogenetic clusters. one that was comprised of the phylotypes from a single termite ... | 2002 | 11866123 |
| viable cytophaga-like bacterium in the 0.2 microm-filtrate seawater. | a strain of the cytophaga-like bacterium (clb), nano-1, was isolated from the 0.2 microm-filtrate of natural seawater. both cellular fatty acid and 16s rdna sequence analyses indicated that nano-1 is closely affiliated to the marine gliding clb genus, microscilla. nano-1 was observed to undergo cyclic morphological change typical of the genus microscilla, and sub-0.2-microm cells were formed in the late stationary phase. the sub-0.2-microm cells were repeatedly revived and subcultured. formation ... | 2001 | 11876369 |
| a mitochondrial-like aconitase in the bacterium bacteroides fragilis: implications for the evolution of the mitochondrial krebs cycle. | aconitase and isocitrate dehydrogenase (idh) enzyme activities were detected in anaerobically prepared cell extracts of the obligate anaerobe bacteroides fragilis. the aconitase gene was located upstream of the genes encoding the other two components of the oxidative branch of the krebs cycle, idh and citrate synthase. mutational analysis indicates that these genes are cotranscribed. a nonpolar in-frame deletion of the acna gene that encodes the aconitase prevented growth in glucose minimal medi ... | 2002 | 11880608 |
| microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds. | we studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (wadi gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. phormidium- and oscillatoria-like cyanobacterial morphotypes were dominant in the field. bacteria belonging to different groups, mainly the cytophaga-flavobacterium-bacteriodes group, the gamma and beta subclasses of the class p ... | 2002 | 11916684 |
| microheterogeneity in 16s ribosomal dna-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations. | temporal changes of the bacterioplankton from a meromictic lake (lake vilar, banyoles, spain) were analyzed with four culture-independent techniques: epifluorescence microscopy, pcr-denaturing gradient gel electrophoresis (dgge) fingerprinting, fluorescence in situ whole-cell hybridization and flow cytometry sorting. microscopically, blooms of one cyanobacterium (synechococcus sp.-like), one green sulfur bacterium (chlorobium phaeobacteroides-like), and one purple sulfur bacterium (thiocystis mi ... | 2002 | 11916688 |