Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
|---|
| molecular characterization of bacterial diversity in lodgepole pine (pinus contorta) rhizosphere soils from british columbia forest soils differing in disturbance and geographic source. | rhizosphere bacteria from lodgepole pine (pinus contorta) seedlings were characterized from forest soils which differed in disturbance and geographic source. soil disturbance treatments included whole-tree harvesting with and without heavy soil compaction and whole-tree harvesting with complete surface organic matter removal and heavy soil compaction from british columbia (bc) ministry of forests long-term soil productivity installations in three biogeoclimatic subzones in central bc, canada. ba ... | 2002 | 19709294 |
| phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete paralvinella palmiformis. | as part of an ongoing examination of microbial diversity associated with hydrothermal vent polychaetes of the family alvinellidae, we undertook a culture-independent molecular analysis of the bacterial assemblage associated with mucous secretions of the northeastern pacific vent polychaete paralvinella palmiformis. using a molecular 16s rdna-based phylogenetic approach, clone libraries were constructed from two samples collected from active sulfide edifices in two hydrothermal vent fields. in bo ... | 2002 | 19709305 |
| effects of copper amendment on the bacterial community in agricultural soil analyzed by the t-rflp technique. | abstract the impact of copper amendment on the bacterial community in agricultural soil was investigated by a 2-year field experiment complemented by short-term microcosm studies. in the field, the amendments led to total copper contents that were close to the safety limits laid down by european authorities. in parallel, bioavailable copper was determined with a copper-specific bioluminescent pseudomonas reporter strain. the amounts of total cu as well as of bioavailable cu in the field declined ... | 2003 | 19719582 |
| isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a sphagnum peat bog. | two dense and highly enriched (up to 10(9) cells ml(-1), <10% of bacterial satellites) acido-tolerant (ph 4.0-6.5) methanogenic consortia, '26' and 'k', were isolated from the peat beneath a sphagnum-eriophorum-carex community in west siberia. both consortia produced methane from co2:h2 on chemically defined, diluted n-free media containing ti(iii)citrate as reducing agent. the phylogenetic analysis of 16s ribosomal dna revealed three archaeal and nine bacterial sequence types. consortium '26' c ... | 2003 | 19719599 |
| bacterioplankton community diversity in a maritime antarctic lake, determined by culture-dependent and culture-independent techniques. | abstract the biodiversity of the pelagic bacterioplankton community of a maritime antarctic freshwater lake was examined by cultivation-dependent and cultivation-independent techniques to determine predominant bacterioplankton populations present. the culture-dependent techniques used were direct culture and observation, polymerase chain reaction amplification of 16s rrna gene fragments, restriction fragment length polymorphism (rflp) analysis followed by selective sequencing and fatty acid meth ... | 2003 | 19719607 |
| bacteria associated with sardine (sardina pilchardus) eggs in a natural environment (ría de vigo, galicia, northwestern spain). | abstract the present study was undertaken to describe the epiflora of the eggs of an important fishing species collected in a coastal zone. microflora associated with sardine (sardina pilchardus) eggs collected in the ría de vigo was examined from january to june 2000. the count was carried out in three different ways: a total direct count by epifluorescence, a heterotrophic bacteria count on marine agar (ma) and a total vibrio count on thiosulfate citrate bile sucrose (tcbs). it was observed th ... | 2003 | 19719614 |
| salinity as a structuring factor for the composition and performance of bacterioplankton degrading riverine doc. | abstract the impact of salinity on the composition and functional performance (biomass production, growth efficiency and growth rates) of bacterial communities was investigated using batch cultures growing on dissolved organic carbon from a river draining into the northern baltic sea. the cultures were adjusted to riverine or estuarine salinity levels and inoculated with bacteria from these two environments. bacterial growth efficiencies differed in response to salinity and the origin of the ino ... | 2003 | 19719630 |
| design and evaluation of group-specific oligonucleotide probes for quantitative analysis of intestinal ecosystems: their application to assessment of equine colonic microflora. | nine oligonucleotide probes complementary to conserved regions of small subunit rrna from phylogenetically defined clusters of intestinal anaerobic bacteria were designed and evaluated for use in quantitative analysis of intestinal microflora. optimum wash temperatures (t(w)) were determined according to the temperature of dissociation (t(d)) of each probe and target group specificity was demonstrated by comparing hybridisation to target and non-target rrna immobilised on nylon membranes. three ... | 2003 | 19719641 |
| activity and distribution of bacterial populations in middle atlantic bight shelf sands. | abstract spatiotemporal variation and metabolic activity of the microbial community were studied in coarse-grained middle atlantic bight shelf sediments in relation to pools of dissolved and particulate carbon. algal cells were present 8->70 mum) fraction of the sediment held the major share (61-98%) of benthic bacteria. bacterial and algal cell abundances, exoenzymatic activity, and [doc] generally showed higher values in may/july 2001 than in august/december 2000. carbohydrates and proteins we ... | 2003 | 19719654 |
| molecular sequence analysis of prokaryotic diversity in the anoxic sediments underlying cyanobacterial mats of two hypersaline ponds in mediterranean salterns. | abstract small-subunit (16s) ribosomal dna clone libraries were constructed using dna isolated from the anoxic sediments underlying the cyanobacterial mats from two sampling stations of different salinity (station a, 150-200 per thousand salinity; station b, 250-320 per thousand salinity) located in the mediterranean salterns of salin-de-giraud (france). previous studies have shown that the mats at these two sites differ greatly in physicochemical and microbial composition. sequence analysis of ... | 2003 | 19719657 |
| bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and dgge analysis. | abstract physiologic activity and community structure of planktonic and biofilm microbial communities in an urban river were analyzed using 5-cyano-2,3-ditolyl tetrazolium chloride (ctc) staining, fluorescent in situ hybridization (fish) and denaturing gradient gel electrophoresis (dgge) analysis of polymerase chain reaction (pcr)-amplified 16s rdna fragments. respiring bacteria estimated by ctc reduction were higher in biofilms (20%) than in stream water samples (12%). fish analysis revealed th ... | 2003 | 19719701 |
| microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16s rrna-targeting oligonucleotide probes. | a study was conducted to investigate the microbial community structure, the physicochemical properties, and the relationships between these parameters of a full-scale industrial biofilter used for waste gas abatement in an animal-rendering plant. fluorescence in situ hybridization (fish) was successfully combined with digital image analysis to study the composition of the microbial community. several new nucleic acid probes were designed and established based on published 16s rdna sequences and ... | 2003 | 12588298 |
| use of a packed-column bioreactor for isolation of diverse protease-producing bacteria from antarctic soil. | seventy-five aerobic heterotrophs have been isolated from a packed-column bioreactor inoculated with soil from antarctica. the column was maintained at 10 degrees c and continuously fed with a casein-containing medium to enrich protease producers. twenty-eight isolates were selected for further characterization on the basis of morphology and production of clearing zones on skim milk plates. phenotypic tests indicated that the strains were mainly psychrotrophs and presented a high morphological a ... | 2003 | 12620829 |
| bacterial rrna genes associated with soil suppressiveness against the plant-parasitic nematode heterodera schachtii. | the goal of this study was to identify bacteria involved in soil suppressiveness against the plant-parasitic nematode heterodera schachtii. since h. schachtii cysts isolated from the suppressive soil can transfer this beneficial property to nonsuppressive soils, analysis of the cyst-associated microorganisms should lead to the identification of the causal organisms. our experimental approach was to identify bacterial rrna genes (rdna) associated with h. schachtii cysts obtained from soil mixture ... | 2003 | 12620845 |
| reichenbachia agariperforans gen. nov., sp. nov., a novel marine bacterium in the phylum cytophaga-flavobacterium-bacteroides. | a heterotrophic, pigmented, agarolytic, gliding bacterium was isolated from a seawater sample collected from the gulf of peter the great, sea of japan, during june 2000. 16s rdna sequence analysis indicated that the novel bacterium, strain kmm 3525t, was a member of the phlyum cytophaga-flavobacterium-bacteroides. on the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, it is proposed that the marine bacterium represents the sole species of a novel genus, reichenbachia, the t ... | 2003 | 12656156 |
| chryseobacterium defluvii sp. nov., isolated from wastewater. | a gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterium (strain b2t) isolated from wastewater of a sequence batch reactor showing enhanced phosphorus removal was investigated to determine its taxonomic status. complete 16s rrna gene sequence analysis indicated that the organism should be placed in the genus chryseobacterium. the strain contained a polyamine pattern with sym-homospermidine as the major compound, menaquinone mk-6 as the predominant menaquinone and ai-c15:0, i-c1 ... | 2003 | 12656158 |
| high diversity among feather-degrading bacteria from a dry meadow soil. | the aim of this study was to determine the diversity of cultivable bacteria able to degrade feathers and present in soil under temperate climate. we obtained 33 isolates from soil samples, which clustered in 13 ardra groups. these isolates were able to grow on solid medium with pigeon feathers as sole carbon and nitrogen source. one representative isolate of each ardra group was selected for identification and feather degradation tests. the phylogenetic analysis of 16s rdna gene fragments reveal ... | 2003 | 12658523 |
| genetic profiling of noncultivated bacteria from the rhizospheres of sugar beet (beta vulgaris) reveal field and annual variability but no effect of a transgenic herbicide resistance. | in this field study, we compared the bacterial communities inhabiting the rhizosphere of a transgenic, herbicide-resistant sugar beet (beta vulgaris) cultivar with those of its nonengineered counterpart, using a genetic profiling technique based on pcr amplifications of partial 16s rrna gene sequences and single-strand conformation polymorphism (sscp). as a control for the plasticity of the bacterial community, we also analyzed the influence of herbicides, the field heterogeneity, and the annual ... | 2003 | 12674342 |
| extraordinary proliferation of microorganisms in aposymbiotic pea aphids, acyrthosiphon pisum. | aposymbiotic pea aphids, which were deprived of their intracellular symbiotic bacterium, buchnera, exhibit growth retardation and no fecundity. high performance liquid chromatographic (hplc) analysis revealed that these aposymbiotic aphids, when reared on broad bean plants, accumulated a large amount of histamine. to assess the possibility of extraordinary proliferation of microorganisms other than buchnera, we enumerated eubacteria and fungi in aphids using the real-time quantitative pcr method ... | 2003 | 12676551 |
| spatial and temporal analysis of the microbial community in slow sand filters used for treating horticultural irrigation water. | an experimental slow sand filter (ssf) was constructed to study the spatial and temporal structure of a bacterial community suppressive to an oomycete plant pathogen, phytophthora cryptogea. passage of water through the mature sand column resulted in complete removal of zoospores of the plant pathogen. to monitor global changes in the microbial community, bacterial and fungal numbers were estimated on selective media, direct viable counts of fungal spores were made, and the atp content was measu ... | 2003 | 12676691 |
| bacterioplankton community shifts in an arctic lake correlate with seasonal changes in organic matter source. | seasonal shifts in bacterioplankton community composition in toolik lake, a tundra lake on the north slope of alaska, were related to shifts in the source (terrestrial versus phytoplankton) and lability of dissolved organic matter (dom). a shift in community composition, measured by denaturing gradient gel electrophoresis (dgge) of 16s rrna genes, occurred at 4 degrees c in near-surface waters beneath seasonal ice and snow cover in spring. this shift was associated with an annual peak in bacteri ... | 2003 | 12676708 |
| improving the thermostability of raw-starch-digesting amylase from a cytophaga sp. by site-directed mutagenesis. | a heat-stable raw-starch-digesting amylase (rsda) was generated through pcr-based site-directed mutagenesis. at 65 degrees c, the half-life of this mutant rsda, which, compared with the wild-type rsda, lacks amino acids r178 and g179, was increased 20-fold. while the wild type was inactivated completely at ph 3.0, the mutant rsda still retained 41% of its enzymatic activity. the enhancement of rsda thermostability was demonstrated to be via a ca(2+)-independent mechanism. | 2003 | 12676725 |
| occupational lung disease related to cytophaga endotoxin exposure in a nylon plant. | workers at a nylon plant developed pulmonary disease with systemic symptoms. differentiating between humidifier fever and hypersensitivity pneumonitis (hp) is challenging. cytophaga, an endotoxin-producing bacteria, was isolated from the plant air-conditioning system. a number of workers had systemic and pulmonary symptoms. precipitins to cytophaga endotoxin were identified. several workers underwent lung biopsies demonstrating hp. inhalation challenges with purified cytophaga endotoxin were per ... | 2003 | 12708142 |
| specificity in the settlement -- modifying response of bacterial biofilms towards zoospores of the marine alga enteromorpha. | previous studies have shown that the rate of settlement of zoospores of the green alga enteromorpha is stimulated by mixed microbial biofilms and that the number of zoospores settling is positively correlated with the number of bacteria in the biofilm. in the present study the specificity of this relationship has been investigated. ninety-nine strains of marine bacteria were isolated from natural biofilms on rocks and the surface of enteromorpha plants. isolates were screened by denaturing gradi ... | 2003 | 12713460 |
| microbial diversity in a thermophilic aerobic biofilm process: analysis by length heterogeneity pcr (lh-pcr). | a two-stage pilot-scale thermophilic aerobic suspended carrier biofilm process (scbp) was set up for the on-site treatment of pulp and paper mill whitewater lining. the microbial diversity in this process was analyzed by length heterogeneity analysis of pcr-amplified 16s ribosomal dna. the primer pair selected for pcr amplification was first evaluated by a computational analysis of fragment lengths in ten main phylogenetical eubacterial groups. the fragment contained the first third of the 16s r ... | 2003 | 12727234 |
| are readily culturable bacteria in coastal north sea waters suppressed by selective grazing mortality? | we studied the growth of six culturable bacterial lineages from coastal north sea picoplankton in environmental samples under different incubation conditions. the grazing pressure of heterotrophic nanoflagellates (hnf) was reduced either by double prefiltration through 0.8- micro m-pore-size filters or by 10-fold dilutions with 0.2- micro m (pore-size) prefiltered seawater. we hypothesized that those gamma-proteobacterial genera that are rapidly enriched would also be most strongly affected by h ... | 2003 | 12732530 |
| bacterioplankton community structure in a maritime antarctic oligotrophic lake during a period of holomixis, as determined by denaturing gradient gel electrophoresis (dgge) and fluorescence in situ hybridization (fish). | the bacterioplankton community structure in moss lake, a maritime antarctic oligotrophic lake, was determined with vertical depth in the water column, during the ice-free period on signy island in the south orkney islands. bacterioplankton community structure was determined using a combination of direct counting of 4',6-diamidino-2-phenylindole (dapi) stained cells, pcr amplification of 16s rrna gene fragments, denaturing gradient gel electrophoresis (dgge) and in situ hybridization with group-s ... | 2003 | 12739078 |
| enumeration of bacteroides species in human faeces by fluorescent in situ hybridisation combined with flow cytometry using 16s rrna probes. | bacteroides is a predominant group of the faecal microbiota in healthy adults. to investigate the species composition of bacteroides by fluorescent in situ hybridisation (fish) combined with flow cytometry, we developed five species-specific probes targeting the 16s rrna. probes were designed to identify cells belonging to bacteroides distasonis, b. fragilis, b. ovatus, b. vulgatus and b. putredinis. the species-specificity of the probes was assessed against a collection of reference strains fro ... | 2003 | 12747418 |
| carriage of potentially fish-pathogenic bacteria in sparus aurata cultured in mediterranean fish farms. | a bacteriological survey of gilthead sea bream sparus aurata from different fish farms and culture systems on the spanish mediterranean coast was conducted. three different studies were performed. study a included hatchery-reared larvae; study b, periodic examination of randomly sampled growing fish; and study c, growing fish sampled only during mortality/morbidity events. in studies b and c, sea cages, earth ponds and indoor tanks were surveyed, and in both cases diseased (showing clinical sign ... | 2003 | 12747637 |
| thermostable aspartase from a marine psychrophile, cytophaga sp. kuc-1: molecular characterization and primary structure. | we found that a psychrophilic bacterium isolated from antarctic seawater, cytophaga sp. kuc-1, abundantly produces aspartase [ec4.3.1.1], and the enzyme was purified to homogeneity. the molecular weight of the enzyme was estimated to be 192,000, and that of the subunit was determined to be 51,000: the enzyme is a homotetramer. l-aspartate was the exclusive substrate. the optimum ph in the absence and presence of magnesium ions was determined to be ph 7.5 and 8.5, respectively. the enzyme was act ... | 2003 | 12761198 |
| combining culture-dependent and -independent methodologies for estimation of richness of estuarine bacterioplankton consuming riverine dissolved organic matter. | three different methods for analyzing natural microbial community diversity were combined to maximize an estimate of the richness of bacterioplankton catabolizing riverine dissolved organic matter (rdom). we also evaluated the ability of culture-dependent quantitative dna-dna hybridization, a 16s rrna gene clone library, and denaturing gradient gel electrophoresis (dgge) to detect bacterial taxa in the same sample. forty-two different cultivatable strains were isolated from rich and poor solid m ... | 2003 | 12788769 |
| sugar metabolism in the extremely halophilic bacterium salinibacter ruber. | growth of salinibacter ruber, a red, extremely halophilic bacterium phylogenetically affiliated with the flavobacterium/cytophaga branch of the domain bacteria, is stimulated by a small number of sugars (glucose, maltose, starch at 1 g l(-1)). glucose consumption starts after other substrates have been depleted. glucose metabolism proceeds via a constitutive, salt-inhibited hexokinase and a constitutive salt-dependent nicotinamide adenine dinucleotide phosphate (nadp)-linked glucose-6-phosphate ... | 2003 | 12799004 |
| survivability and long-term preservation of bacteria in water and in phosphate-buffered saline. | to evaluate the suitability of using sterile water and phosphate-buffered saline (pbs) for preservation of bacteria pathogenic to plants or humans. | 2003 | 12803555 |
| biodegradation of mtbe and btex in an aerobic fluidized bed reactor. | an aerobic fluidized bed reactor (fbr) was operated for the removal of methyl tert-butyl (mbe) and benzene, toluene, ethylbenzene, and p-xylene (btex) from water. the reactor was seeded with a mixed culture adapted to mtbe. granular activated carbon (gac) was used as the biological attachment medium. influent mtbe to the reactor was 7.8 mg/l mtbe, with a flow rate of 22.7 l/day, and an empty bed contact time of 1 hour. the acclimation period required was relatively short, about 30 days before re ... | 2003 | 12830950 |
| heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations. | batch cultures of aquatic bacteria and dissolved organic matter were used to examine the impact of carbon source concentration on bacterial growth, biomass, growth efficiency, and community composition. an aged concentrate of dissolved organic matter from a humic lake was diluted with organic compound-free artificial lake water to obtain concentrations of dissolved organic carbon (doc) ranging from 0.04 to 2.53 mm. the bacterial biomass produced in the cultures increased linearly with the doc co ... | 2003 | 12839735 |
| identification of a new ribosomal protection type of tetracycline resistance gene, tet(36), from swine manure pits. | previously, only one ribosome protection type of a tetracycline resistance gene, tetq, had been identified in bacteroides spp. during an investigation of anaerobic bacteria present in swine feces and manure storage pits, a tetracycline-resistant bacteroides strain was isolated. subsequent analysis showed that this new bacteroides strain, bacteroides sp. strain 139, did not contain tetq but contained a previously unidentified tetracycline resistance gene. sequence analysis showed that the tetracy ... | 2003 | 12839793 |
| novel psychrophilic and thermolabile l-threonine dehydrogenase from psychrophilic cytophaga sp. strain kuc-1. | a psychrophilic bacterium, cytophaga sp. strain kuc-1, that abundantly produces a nad(+)-dependent l-threonine dehydrogenase was isolated from antarctic seawater, and the enzyme was purified. the molecular weight of the enzyme was estimated to be 139,000, and that of the subunit was determined to be 35,000. the enzyme is a homotetramer. atomic absorption analysis showed that the enzyme contains no metals. in these respects, the cytophaga enzyme is distinct from other l-threonine dehydrogenases t ... | 2003 | 12867457 |
| sulfate-reducing bacterial community structure and their contribution to carbon mineralization in a wastewater biofilm growing under microaerophilic conditions. | the community structure of sulfate-reducing bacteria (srb) and the contribution of srb to carbon mineralization in a wastewater biofilm growing under microaerophilic conditions were investigated by combining molecular techniques, molybdate inhibition batch experiments, and microelectrode measurements. a 16s rdna clone library of bacteria populations was constructed from the biofilm sample. the 102 clones analyzed were grouped into 53 operational taxonomic units (otus), where the clone distributi ... | 2003 | 12879306 |
| cloning and functional expression of dipeptidyl peptidase iv from the ruminal bacterium prevotella albensis m384(t). | ruminal bacteria of the genus prevotella play a crucial role in peptide breakdown in the rumen, a component of protein catabolism that leads to the inefficient use of dietary protein by ruminant animals. this is the first report of the cloning of a peptidase gene from a ruminal bacterium. part of the dipeptidyl peptidase type iv (dpp-iv) gene from prevotella albensis m384(t) was cloned using degenerate primers designed from conserved regions found within other known dpp-iv sequences. flanking re ... | 2003 | 12904562 |
| high 16s rdna bacterial diversity in glacial meltwater lake sediment, bratina island, antarctica. | the microbial diversity in maritime meltwater pond sediments from bratina island, ross sea, antarctica was investigated by 16s rdna-dependent molecular phylogeny. investigations of the vertical distribution, phylogenetic composition, and spatial variability of bacteria and archaea in the sediment were carried out. results revealed the presence of a highly diverse bacterial population and a significantly depth-related composition. assessment of 173 partial 16s rdna clones analyzed by amplified rd ... | 2003 | 12910387 |
| molecular characterization of the microbial species that colonize human ileal and colonic mucosa by using 16s rdna sequence analysis. | the aim of this study was to characterize the bacterial community adhering to the mucosa of the terminal ileum, and proximal and distal colon of the human digestive tract. | 2003 | 12911699 |
| application of comparative genomics in the identification and analysis of novel families of membrane-associated receptors in bacteria. | a great diversity of multi-pass membrane receptors, typically with 7 transmembrane (tm) helices, is observed in the eukaryote crown group. so far, they are relatively rare in the prokaryotes, and are restricted to the well-characterized sensory rhodopsins of various phototropic prokaryotes. | 2003 | 12914674 |
| isolation, characterization and comparison of bacteria from swine faeces and manure storage pits. | storage of swine manure is associated with the microbiological production of a variety of odorous chemicals including ammonia, organic acids and alcohols, and sulphides. although largely the product of microbiological activity, little is known about the microorganisms present in swine manure. in order to gain a better understanding of the types and activities of the microorganisms present, representative strains of microorganisms were isolated from faeces and stored manure slurry, identified, an ... | 2003 | 12919409 |
| complete genome sequence of the oral pathogenic bacterium porphyromonas gingivalis strain w83. | the complete 2,343,479-bp genome sequence of the gram-negative, pathogenic oral bacterium porphyromonas gingivalis strain w83, a major contributor to periodontal disease, was determined. whole-genome comparative analysis with other available complete genome sequences confirms the close relationship between the cytophaga-flavobacteria-bacteroides (cfb) phylum and the green-sulfur bacteria. within the cfb phyla, the genomes most similar to that of p. gingivalis are those of bacteroides thetaiotaom ... | 2003 | 12949112 |
| bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring. | an artesian sulfide- and sulfur-rich spring in southwestern oklahoma is shown to sustain an extremely rich and diverse microbial community. laboratory incubations and autoradiography studies indicated that active sulfur cycling is occurring in the abundant microbial mats at zodletone spring. anoxygenic phototrophic bacteria oxidize sulfide to sulfate, which is reduced by sulfate-reducing bacterial populations. the microbial community at zodletone spring was analyzed by cloning and sequencing 16s ... | 2003 | 12957951 |
| incidence of a new sex-ratio-distorting endosymbiotic bacterium among arthropods. | many intracellular micro-organisms are now known to cause reproductive abnormalities and other phenomena in their hosts. the endosymbiont wolbachia is the best known of these reproductive manipulators owing to its extremely high incidence among arthropods and the diverse host effects it has been implicated as causing. however, recent evidence suggests that another intracellular bacterium, a cytophaga-like organism (clo), may also induce several reproductive effects in its hosts. here, we present ... | 2003 | 12964989 |
| biodegradation of an alicyclic hydrocarbon by a sulfate-reducing enrichment from a gas condensate-contaminated aquifer. | we used ethylcyclopentane (ecp) as a model alicyclic hydrocarbon and investigated its metabolism by a sulfate-reducing bacterial enrichment obtained from a gas condensate-contaminated aquifer. the enrichment coupled the consumption of ecp with the stoichiometrically expected amount of sulfate reduced. during ecp biodegradation, we observed the transient accumulation of metabolite peaks by gas chromatography-mass spectrometry, three of which had identical mass spectrometry profiles. mass-spectral ... | 2003 | 12514025 |
| rapid detection of columnaris disease in channel catfish (ictalurus punctatus) with a new species-specific 16-s rrna gene-based pcr primer for flavobacterium columnare. | a 16-s rrna gene from the chromosomal dna of the fish-pathogenic bacterium flavobacterium columnare (formerly flexibacter columnaris), strain ars-i, was cloned, sequenced and used to design a polymerase chain reaction (pcr) primer set. the primer set amplified a specific 1193-bp dna fragment from f. columnare strains but not from related bacteria, f. psychrophilum, f. aquatile, f. branchiophilum, or other bacterial pathogens of fish, flexibacter maritimus, cytophaga johnsonae, edwardsiella ictal ... | 2003 | 12459241 |
| a simple method for dna extraction from marine bacteria that produce extracellular materials. | we present a simple method for extracting dna from the marine bacteria hahella chejuensis, a streptomyces sp., and a cytophaga sp. previously, dna purification from these strains was hindered by the presence of extracellular materials. in our extraction method, the marine bacteria are lysed by freezing and grinding in liquid nitrogen, and treated with sds. the extracted dna is purified using a phenol/chloroform mixture, and precipitated in isopropanol. the extracted dna is of high quality and su ... | 2003 | 12459245 |
| isolation and phylogenetic characterization of bacteria capable of inducing differentiation in the green alga monostroma oxyspermum. | many green algae cannot develop normally when they are grown under axenic conditions. monostroma oxyspermum, for example, proliferates unicellularly in an aseptic culture, but develops into a normal foliaceous gametophyte in the presence of some marine bacteria. more than 1000 bacterial strains were isolated from marine algae and sponges and assayed for their ability to induce the morphogenesis of unicellular m. oxyspermum. fifty bacterial strains exhibiting morphogenesis-inducing activity again ... | 2003 | 12542710 |
| depth distribution of microbial diversity in mono lake, a meromictic soda lake in california. | we analyzed the variation with depth in the composition of members of the domain bacteria in samples from alkaline, hypersaline, and currently meromictic mono lake in california. dna samples were collected from the mixolimnion (2 m), the base of the oxycline (17.5 m), the upper chemocline (23 m), and the monimolimnion (35 m). composition was assessed by sequencing randomly selected cloned fragments of 16s rrna genes retrieved from the dna samples. most of the 212 sequences retrieved from the sam ... | 2003 | 12571026 |
| dynamics of microcystin-degrading bacteria in mucilage of microcystis. | to reveal the process of degradation of hepatotoxic microcystin produced in microcystis cells during the microcystis bloom period, we used fluorescence in situ hybridization (fish) to analyze the population dynamics of microcystin-degrading bacteria in microcystis mucilage. we designed and applied an oligonucleotide probe targeted to the 16s rrna sequence of strain y2 of a microcystin-degrading bacterium (mcd-bacterium), which was isolated from lake suwa, japan. in both the 1998 and 1999 tests, ... | 2003 | 14708752 |
| vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum cytophaga-flavobacterium-bacteroides. | a novel heterotrophic, yellow-orange-pigmented, non-motile, asporogenic, strictly aerobic, gram-negative, oxidase and catalase-positive bacterium kmm 3516(t) was isolated from the holothurian apostichopus japonicus collected from troitsa bay in the gulf of peter the great (sea of japan) during november 1997. 16s rdna sequence analysis revealed that strain kmm 3516(t) was a member of the family flavobacteriaceae: the dna g+c content of kmm 3516(t) was 41.3 mol%. major respiratory quinone was mk-6 ... | 2003 | 13130007 |
| [isolation of hydrocarbon-oxidizing psychrophilic bacteria from oil-polluted soils]. | microorganisms growing on a mineral medium with crude oil and its light fractions as only carbon and energy sources have been isolated from samples of oil-polluted soils collected in the usa district (komi republic, russia). for the first time, hydrocarbon-oxidizing psychrophilic bacteria of the genus cytophaga have been found that are clearly capable of consuming crude oil hydrocarbons. a method for cultivating microorganisms on porous plastic is proposed. the data from the literature on the re ... | 2003 | 14714480 |
| evolutionary relationships among photosynthetic bacteria. | to understand the evolution of photosynthetic bacteria it is necessary to understand how the main groups within bacteria have evolved from a common ancestor, a critical issue that has not been resolved in the past. recent analysis of shared conserved inserts or deletions (indels) in protein sequences has provided a powerful means to resolve this long-standing problem in microbiology. based on a set of 25 indels in highly conserved and widely distributed proteins, all main groups within bacteria ... | 2003 | 16228576 |
| comparative 16s rdna and 16s rrna sequence analysis indicates that actinobacteria might be a dominant part of the metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. | bacterial diversity in 16s ribosomal dna and reverse-transcribed 16s rrna clone libraries originating from the heavy metal-contaminated rhizosphere of the metal-hyperaccumulating plant thlaspi caerulescens was analysed and compared with that of contaminated bulk soil. partial sequence analysis of 282 clones revealed that most of the environmental sequences in both soils affiliated with five major phylogenetic groups, the actinobacteria, alpha-proteobacteria, beta-proteobacteria, acidobacteria an ... | 2003 | 14510843 |
| bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the mid-atlantic ridge. | we report here a molecular survey based on 16s rrna genes of the bacterial diversity found in two deep-sea vent niches at the mid-atlantic ridge: hydrothermal sediment (rainbow site), and microcolonizers made of three different substrates (organic-rich, iron-rich and pumice) that were exposed for 15 days to a vent emission. bacterial diversity in sediment samples was scattered through many bacterial divisions. the most abundant and diverse environmental sequences (phylotypes) in our libraries co ... | 2003 | 14510850 |
| [comparative study of microbial communities from cultured and natural population of the mussel mytilus trossulus in peter the great bay]. | the 525 strains of heterotrophic bacteria isolated from natural and cultured populations of the mussel mytilus trossulus and the surrounding seawater were identified to a genus level on the basis of phenotypic analysis and the fatty acid composition of cell lipids. gram-negative isolates were dominated by six genera of the family enterobacteriaceae and by the genera pseudoalteromonas, vibrio, photobacterium, cytophaga/flavobacterium/bacteroides, pseudomonas, and moraxella, gram-positive isolates ... | 2003 | 14526545 |
| phylogenetic diversity, abundance, and axial distribution of bacteria in the intestinal tract of two soil-feeding termites (cubitermes spp.). | the hindgut of soil-feeding termites is highly compartmentalized and characterized by pronounced axial dynamics of the intestinal ph and microbial processes such as hydrogen production, methanogenesis, and reductive acetogenesis. nothing is known about the bacterial diversity and the abundance or axial distribution of the major phylogenetic groups in the different gut compartments. in this study, we showed that the variety of physicochemical conditions is reflected in the diversity of the microb ... | 2003 | 14532056 |
| the trove module: a common element in telomerase, ro and vault ribonucleoproteins. | ribonucleoproteins carry out a variety of important tasks in the cell. in this study we show that a number of these contain a novel module, that we speculate mediates rna-binding. | 2003 | 14563212 |
| flavobacterium johnsoniae gldh is a lipoprotein that is required for gliding motility and chitin utilization. | cells of flavobacterium johnsoniae move rapidly over surfaces by gliding motility. the mechanism of this form of motility is not known. six genes (glda, gldb, gldd, gldf, gldg, and ftsx) that are required for gliding have been described. tn4351 mutagenesis was used to identify another gene, gldh, which is required for cell movement. gldh mutants formed nonspreading colonies, and individual cells lacked the cell movements and ability to propel latex spheres along their surfaces that are character ... | 2003 | 14594839 |
| starvation of flavobacterium psychrophilum in broth, stream water and distilled water. | physical changes in flavobacterium psychrophilum, the causative agent of rainbow trout fry syndrome (rtfs), were examined over a 19 wk period of starvation. bacteria were maintained in either cytophaga broth, filtered stream water, or filtered distilled water, or were maintained in broth after disinfection as a negative control for dead bacteria. culturability and viability of the bacterium were assessed using colony-forming units (cfus) and a commercially available live/dead kit. antigenic prof ... | 2003 | 14598987 |
| diversity and abundance of uncultured cytophaga-like bacteria in the delaware estuary. | the cytophaga-flavobacterium group is known to be abundant in aquatic ecosystems and to have a potentially unique role in the utilization of organic material. however, relatively little is known about the diversity and abundance of uncultured members of this bacterial group, in part because they are underrepresented in clone libraries of 16s rrna genes. to circumvent a suspected bias in pcr, a primer set was designed to amplify 16s rrna genes from the cytophaga-flavobacterium group and was used ... | 2003 | 14602617 |
| diversity and structure of bacterial communities in arctic versus antarctic pack ice. | a comprehensive assessment of bacterial diversity and community composition in arctic and antarctic pack ice was conducted through cultivation and cultivation-independent molecular techniques. we sequenced 16s rrna genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively. most of the 33 arctic phylotypes were >97% identical to previously described antarctic species or to our own antarctic isolates. at both poles, the alpha- and gamma-proteobacteri ... | 2003 | 14602620 |
| microbial community structure in midgut and hindgut of the humus-feeding larva of pachnoda ephippiata (coleoptera: scarabaeidae). | the guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. in a companion paper (t. lemke, u. stingl, m. egert, m. w. friedrich, and a. brune, appl. environ. microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and ... | 2003 | 14602626 |
| phylogenetic analysis of fiber-associated rumen bacterial community and pcr detection of uncultured bacteria. | the fiber-associated rumen bacterial community was phylogenetically examined by analysis of 16s rrna gene (16s rdna) sequences. hay stems of orchardgrass and alfalfa were incubated for 6 and 20 h, respectively in the rumen of two different sheep, and total dna was extracted from the incubated stems to clone bacterial 16s rdnas using polymerase chain reaction (pcr). of 91 such clones, 21 showed more than 97% sequence similarity with known isolates, 32 clones had 90-97% similarity with known seque ... | 2003 | 14659538 |
| metagenome survey of biofilms in drinking-water networks. | most naturally occurring biofilms contain a vast majority of microorganisms which have not yet been cultured, and therefore we have little information on the genetic information content of these communities. therefore, we initiated work to characterize the complex metagenome of model drinking water biofilms grown on rubber-coated valves by employing three different strategies. first, a sequence analysis of 650 16s rrna clones indicated a high diversity within the biofilm communities, with the ma ... | 2003 | 14660379 |
| culture-independent phylogenetic analysis of the faecal flora of the rat. | the dominant faecal flora of the rat was determined using randomly cloned 16s rdna comparative sequence analysis. a total of 109 near full-length 16s rdna clones were sequenced, representing 69 unique 16s rrna phylotypes or operational taxonomic units (otus). estimates of species richness indicated that approximately 338 species were present in the faeces, suggesting that only 20% of species were identified. only two of 39 gram-negative clones aligned with previously cultured species, the remain ... | 2003 | 14663493 |
| the microbial community analysis of a 5-stage bnr process with step feed system. | the microbial communities of 5-stage bnr activated sludge samples were analyzed using fluorescence in-situ hybridization (fish) and 16s rdna characterization. the total cell numbers of each reactor were from 2.36 x 10(9) cells/ml to 2.83 x 10(9) cells/ml. from 56.5% to 62.0% of total dapi cell counts were hybridized to the most bacterial specific probe eub 338. among them, beta-proteobacteria were most dominant in each tank. the number of phosphate accumulating organisms (paos) was almost 50% of ... | 2003 | 14682580 |
| molecular microbiology of gut bacteria: genetic diversity and community structure analysis. | recently developed molecular biology approaches make possible the detailed genetic, taxonomic and ecological examination of microorganisms from various habitats. animal gut represents one of the most complex microbial ecosystems with a large degree of microbial biodiversity present. bacteria inhabiting the gut usually play important roles in metabolic transformations of substrates and sometimes, e.g. in ruminants, they make the basis for an obligate symbiosis with the host. here we discuss molec ... | 2003 | 14750440 |
| metamorphosis of a scleractinian coral in response to microbial biofilms. | microorganisms have been reported to induce settlement and metamorphosis in a wide range of marine invertebrate species. however, the primary cue reported for metamorphosis of coral larvae is calcareous coralline algae (cca). herein we report the community structure of developing coral reef biofilms and the potential role they play in triggering the metamorphosis of a scleractinian coral. two-week-old biofilms induced metamorphosis in less than 10% of larvae, whereas metamorphosis increased sign ... | 2004 | 14766608 |
| early steps in microbial colonization processes at deep-sea hydrothermal vents. | a pluri-disciplinary in situ colonization experiment was performed to study early stages of colonization in deep-sea vent alvinella spp. worm habitats. four colonization devices were deployed onto alvinella spp. colonies of different chimneys of the east-pacific rise (epr 13 degrees n), for two different periods: a short (less than a week) and a longer one (3 weeks). video imagery and monitoring of the thermal and physico-chemical conditions were performed during the colonization experiments. nu ... | 2004 | 14871207 |
| diverse microbial communities inhabit antarctic sponges. | genetic techniques were employed to investigate the archaeal, bacterial and eukaryotic communities associated with the antarctic sponges kirkpatrickia varialosa, latrunculia apicalis, homaxinella balfourensis, mycale acerata and sphaerotylus antarcticus. the phylogenetic affiliation of sponge-derived bacteria was assessed by 16s rrna sequencing of cloned dna fragments. denaturing gradient gel electrophoresis (dgge) was used to determine the stability of bacterial associations within each sponge ... | 2004 | 14871212 |
| sulfate-reducing bacteria-dominated biofilms that precipitate zns in a subsurface circumneutral-ph mine drainage system. | the microbial diversity of zns-forming biofilms in 8 degrees c, circumneutral-ph groundwater in tunnels within the abandoned piquette zn, pb mine (tennyson, wisconsin, usa) has been investigated by molecular methods, fluorescence in situ hybridization (fish), and cultivation techniques. these biofilms are growing on old mine timbers that generate locally anaerobic zones within the mine drainage system. sulfate-reducing bacteria (srb) exclusively of the family desulfobacteriaceae comprise a signi ... | 2004 | 14994175 |
| high-diversity biofilm for the oxidation of sulfide-containing effluents. | in the present work, we describe for the first time the utilization of a complex microbial biofilm for the treatment of sulfide-containing effluents. a non-aerated packed-column reactor was inoculated with anoxic lake sediment and exposed to light. a biofilm developed in the column and showed a stable oxidation performance for several weeks. microbial species composition was analyzed by microscopy, pigment analysis and a bacterial 16s rrna gene clone library. colorless sulfur bacteria, green alg ... | 2004 | 14997354 |
| ecophysiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by microautoradiography-fluorescence in situ hybridization. | ecophysiological interactions between the community members (i.e., nitrifiers and heterotrophic bacteria) in a carbon-limited autotrophic nitrifying biofilm fed only nh(4)(+) as an energy source were investigated by using a full-cycle 16s rrna approach followed by microautoradiography (mar)-fluorescence in situ hybridization (fish). phylogenetic differentiation (identification) of heterotrophic bacteria was performed by 16s rrna gene sequence analysis, and fish probes were designed to determine ... | 2004 | 15006789 |
| tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in skagerrak, denmark. | a number of bacteria were isolated from sea water in skagerrak, denmark, at 30 m depth. two of the isolates, strains d28 and d30(t), belonged to the flavobacteriaceae within the cytophaga-flavobacterium-bacteroides group. sequencing of 16s rrna genes of the two strains indicated strongly that they belonged to the genus tenacibaculum and that they showed greatest similarity to the species tenacibaculum amylolyticum and tenacibaculum mesophilum. dna-dna hybridization values, dna base composition a ... | 2004 | 15023969 |
| glycerol metabolism in the extremely halophilic bacterium salinibacter ruber. | growth of salinibacter ruber, a red, extremely halophilic bacterium phylogenetically affiliated with the flavobacterium/cytophaga branch of the domain bacteria, is stimulated by glycerol. in contrast to glucose consumption, which starts only after more easily degradable substrates present in yeast extract have been depleted, glycerol is consumed during the earliest growth phases. when u-(14)c-labeled glycerol was added to the culture, up to 25% of the radioactivity was incorporated by the cells. ... | 2004 | 15033241 |
| diversity of kenyan soda lake alkaliphiles assessed by molecular methods. | dna was extracted from water and sediment samples taken from soda lakes of the kenyan-tanzanian rift valley. dna was also extracted from microbial enrichment cultures of sediment samples. 16s rrna genes were amplified by the polymerase chain reaction and microbial diversity was studied using denaturing gradient gel electrophoresis (dgge) of 16s rdna amplicons. cloning and sequencing of single dgge bands showed that they usually contained mixed amplicons. several of the amplicon sequences had hig ... | 2004 | 15064991 |
| a population survey of members of the phylum bacteroidetes isolated from salt marsh sediments along the east coast of the united states. | the population diversity of cultured isolates of the phylum bacteroidetes was investigated from salt-marsh sediments. a total of 44 isolates that belonged to this phylum were isolated either from high-dilution plates or from end-dilution most-probable-number (mpn) tubes. the majority of the isolates came from virginia, with others isolated from salt marshes in delaware and north carolina. all the isolates were aerobic gram-negative, catalase positive small rods that formed uniform colonies; most ... | 2004 | 15107955 |
| bacterial communities associated with flowering plants of the ni hyperaccumulator thlaspi goesingense. | thlaspi goesingense is able to hyperaccumulate extremely high concentrations of ni when grown in ultramafic soils. recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet. in this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing t. goesingense were characterized in detail by using both cultivation and cultivation-independent te ... | 2004 | 15128517 |
| seasonal changes in an alpine soil bacterial community in the colorado rocky mountains. | the period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. the large winter microbial community begins to turn over rapidly, releasing nutrients to plants. past studies have shown that the soil microbial community in alpine dry meadows of the colorado rocky mountains changes in biomass, function, broad-level structure, and fungal diversity between winter and early summer. however, little specific information exists on the diversity of the alpine bacterial communit ... | 2004 | 15128545 |
| kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide. | a bacterium (named ot-1(t)) that showed algicidal activity was isolated from sea water of masan bay, korea, during an outbreak of red tide. phylogenetic analysis based on 16s rdna sequences showed that the isolate formed a distinct phyletic lineage within the family flavobacteriaceae of the cytophaga-flavobacterium-bacteroides group. no species with a validly published name showed >/=93 % 16s rrna gene sequence similarity to strain ot-1(t). the isolate had major amounts of iso-branched and 3-hyd ... | 2004 | 15143006 |
| psychroflexus tropicus sp. nov., an obligately halophilic cytophaga-flavobacterium-bacteroides group bacterium from an hawaiian hypersaline lake. | a gram-negative bacterium designated la1(t) was isolated from water collected in hypersaline lake laysan on laysan island in the northwestern hawaiian islands. cells occurred singly as fine rods to short filaments. growth in 50 % strength marine broth occurred optimally when the medium contained 7.5-10 % (w/v) nacl. the major fatty acids in la1(t) grown at 15 and 30 degrees c were 12-methyl tetradecanoic acid and 13-methyl tetradecanoic acid, respectively. the nucleotide sequence of the 16s rrna ... | 2004 | 15143045 |
| characterization of a 'bacteroidetes' symbiont in encarsia wasps (hymenoptera: aphelinidae): proposal of 'candidatus cardinium hertigii'. | previously, analysis of 16s rdna sequences placed a newly discovered lineage of bacterial symbionts of arthropods in the 'bacteroidetes'. this symbiont lineage is associated with a number of diverse host reproductive manipulations, including induction of parthenogenesis in several encarsia parasitoid wasps (hymenoptera: aphelinidae). in this study, electron microscopy and phylogenetic analysis of the 16s rrna and gyrb genes of symbionts from encarsia hispida and encarsia pergandiella are used to ... | 2004 | 15143050 |
| cytophaga-flavobacterium gliding motility. | flavobacterium johnsoniae, like many other members of the cytophaga-flavobacterium-bacteroides group, displays rapid gliding motility. cells of f. johnsoniae glide over surfaces at rates of up to 10 microm/s. latex spheres added to f. johnsoniae bind to and are rapidly propelled along cells, suggesting that adhesive molecules move laterally along the cell surface during gliding. genetic analyses have identified a number of gld genes that are required for gliding. three gld proteins are thought t ... | 2004 | 15170404 |
| competition for polymers among heterotrophic bacteria, isolated from particles of the equatorial atlantic. | three heterotrophic bacterial strains, isolated from organic particles of the upper water column of the equatorial atlantic, taken during a cruise on the r/v meteor (1997), were investigated concerning their physiological and phylogenetic properties using classic microbiological and modern molecular-biological methods. all isolates are gram-negative rods able to use polymers such as cellulose, chitin or starch as sole carbon source. the phylogeny of these isolates was investigated by fluorescenc ... | 2004 | 15179602 |
| signature sequences in diverse proteins provide evidence for the late divergence of the order aquificales. | the aquificales species are presently believed to be the earliest branching lineage within bacteria. however, the branching order of this group in different phylogenetic trees is highly variable and not resolved. in the present work, the phylogenetic placement of aquificales was examined by means of a cladistic approach based on the shared presence or absence of definite signature sequences (consisting of conserved inserts or deletions) in many highly conserved and important proteins, e.g. rna p ... | 2004 | 15179606 |
| evolution of bacterial rna polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. | comparative analysis of the domain architectures of the beta, beta', and sigma(70) subunits of bacterial dna-dependent rna polymerases (ddrp), combined with sequence-based phylogenetic analysis, revealed a fundamental split among bacteria. dna-dependent rna polymerase subunits of group i, which includes proteobacteria, aquifex, chlamydia, spirochaetes, cytophaga-chlorobium, and planctomycetes, are characterized by three distinct inserts, namely a sandwich barrel hybrid motif domain in the beta s ... | 2004 | 15194191 |
| biological hydrogen production using a membrane bioreactor. | a cross-flow membrane was coupled to a chemostat to create an anaerobic membrane bioreactor (mbr) for biological hydrogen production. the reactor was fed glucose (10,000 mg/l) and inoculated with a soil inoculum heat-treated to kill non-spore-forming methanogens. hydrogen gas was consistently produced at a concentration of 57-60% in the headspace under all conditions. when operated in chemostat mode (no flow through the membrane) at a hydraulic retention time (hrt) of 3.3 h, 90% of the glucose w ... | 2004 | 15211496 |
| diversity and cold-active hydrolytic enzymes of culturable bacteria associated with arctic sea ice, spitzbergen. | the diversity of culturable bacteria associated with sea ice from four permanently cold fjords of spitzbergen, arctic ocean, was investigated. a total of 116 psychrophilic and psychrotolerant strains were isolated under aerobic conditions at 4 degrees c. the isolates were grouped using amplified rdna restriction analysis fingerprinting and identified by partial sequencing of 16s rrna gene. the bacterial isolates fell in five phylogenetic groups: subclasses alpha and gamma of proteobacteria, the ... | 2004 | 15252724 |
| increased fecundity associated with infection by a cytophaga-like intracellular bacterium in the predatory mite, metaseiulus occidentalis. | the endosymbiont wolbachia has gained widespread notoriety over the past decade because of its high infection frequency among arthropods, and the unique heterogeneity of the host reproductive effects that it has been implicated as causing to enhance its own spread. recently, another endosymbiotic bacterium from the cytophaga-flavobacterium-bacteroides phylum has been shown to be widespread among arthropods and manipulate its hosts' reproduction to enhance its own spread. we show that infection b ... | 2004 | 15252981 |
| bacterial diversity in malan ice core from the tibetan plateau. | three ice core samples were collected from the malan ice core drilled from the tibetan plateau, and three 16s rdna clone libraries by direct amplification from the ice-melted water were established. ninety-four clones containing bacterial 16s rdna inserts were selected. according to restriction fragment-length polymorphism analysis, 11 clones were unique in the library from which they were obtained and used for partial sequence and phylogenetic analysis, and compared with 8 reported sequences fr ... | 2004 | 15259767 |
| multiple displacement amplification in combination with high-fidelity pcr improves detection of bacteria from single females or eggs of metaseiulus occidentalis (nesbitt) (acari: phytoseiidae). | amplifying microbial dna by the polymerase chain reaction (pcr) from single phytoseiid mites has been difficult, perhaps due to the low titer of bacteria and to interference by the relatively larger amounts of mite genomic dna. in this paper we evaluate the efficiency of standard and high-fidelity pcr protocols subsequent to amplification of the whole genome by a multiple displacement amplification (mda) procedure developed by dean et al. dna from the phytoseiid phytoseiulus persimilis (athias-h ... | 2004 | 15261775 |
| use of microautoradiography combined with fluorescence in situ hybridization to determine dimethylsulfoniopropionate incorporation by marine bacterioplankton taxa. | the fraction of planktonic heterotrophic bacteria capable of incorporating dissolved dimethylsulfoniopropionate (dmsp) and leucine was determined at two coastal sites by microautoradioagraphy (au). in gulf of mexico seawater microcosm experiments, the proportion of prokaryotes that incorporated sulfur from [(35)s]dmsp ranged between 27 and 51% of 4',6-diamidino-2-phenylindole (dapi)-positive cells, similar to or slightly lower than the proportion incorporating [(3)h]leucine. in the northwest med ... | 2004 | 15294798 |
| alkaliflexus imshenetskii gen. nov. sp. nov., a new alkaliphilic gliding carbohydrate-fermenting bacterium with propionate formation from a soda lake. | anaerobic saccharolytic bacteria thriving at high ph values were studied in a cellulose-degrading enrichment culture originating from the alkaline lake, verkhneye beloye (central asia). in situ hybridization of the enrichment culture with 16s rrna-targeted probes revealed that abundant, long, thin, rod-shaped cells were related to cytophaga. bacteria of this type were isolated with cellobiose and five isolates were characterized. isolates were thin, flexible, gliding rods. they formed a spherica ... | 2004 | 15340778 |
| quantifying 3h-thymidine incorporation rates by a phylogenetically defined group of marine planktonic bacteria (bacteriodetes phylum). | the rate of [(3)h-methyl] thymidine ((3)h-tdr) incorporation into dna has been applied extensively to measure cell production by bacterial communities in aquatic environments. here we describe a method to quantify (3)h-tdr incorporation by specific, phylogenetically defined members of the bacterial community. the method involves selectively capturing dna from targeted groups of bacteria and then quantifying its (3)h radioactivity. the method was applied to measure (3)h-tdr incorporation by the m ... | 2004 | 15344931 |
| hongiella marincola sp. nov., isolated from sea water of the east sea in korea. | two gram-negative, non-motile, non-spore-forming, rod-shaped strains, sw-2t and sw-26, were isolated from sea water of the east sea in korea. these organisms grew optimally at 37 degrees c and in the presence of 2-3 % (w/v) nacl. they did not grow without nacl or in the presence of >9 % (w/v) nacl. strains sw-2t and sw-26 were characterized chemotaxonomically as having mk-7 as the predominant isoprenoid quinone and iso-c(15 : 0) as the major fatty acid. the dna g + c content of strains sw-2t and ... | 2004 | 15388753 |
| bacterial community associated with black band disease in corals. | black band disease (bbd) is a virulent polymicrobial disease primarily affecting massive-framework-building species of scleractinian corals. while it has been well established that the bbd bacterial mat is dominated by a cyanobacterium, the quantitative composition of the bbd bacterial mat community has not described previously. terminal-restriction fragment length polymorphism (t-rflp) analysis was used to characterize the infectious bacterial community of the bacterial mat causing bbd. these a ... | 2004 | 15466538 |
| flow sorting of marine bacterioplankton after fluorescence in situ hybridization. | we describe an approach to sort cells from coastal north sea bacterioplankton by flow cytometry after in situ hybridization with rrna-targeted horseradish peroxidase-labeled oligonucleotide probes and catalyzed fluorescent reporter deposition (card-fish). in a sample from spring 2003 >90% of the cells were detected by card-fish with a bacterial probe (eub338). approximately 30% of the microbial assemblage was affiliated with the cytophaga-flavobacterium lineage of the bacteroidetes (cfb group) ( ... | 2004 | 15466568 |