Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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| bloom of filamentous bacteria in a mesotrophic lake: identity and potential controlling mechanism. | ephemeral blooms of filamentous bacteria are a common phenomenon in the water column of oligo- to mesotrophic lakes. it is assumed that the appearance of such morphotypes is favored by selective predation of bacterivorous protists and that filter-feeding zooplankton plays a major role in suppressing these bacteria. the phylogenetic affiliation of the important bloom-forming filamentous bacteria in freshwaters is presently unknown. here we report the identification of dominant members of a filame ... | 2004 | 15466575 |
| microbial community structure in a thermophilic anaerobic hybrid reactor degrading terephthalate. | a thermophilic terephthalate-degrading methanogenic consortium was successfully enriched for 272 days in an anaerobic hybrid reactor, and the microbial structure was characterized using terminal rflps, clone libraries and fluorescence in-situ hybridization with rrna-targeted oligonucleotide probes. all the results suggested that methanothrix thermophila-related methanogens, desulfotomaculum-related bacterial populations in the gram-positive low-g + c group, and op5-related populations were the k ... | 2004 | 15470120 |
| a phylogenetic analysis of wadi el natrun soda lake cellulase enrichment cultures and identification of cellulase genes from these cultures. | samples of sediments and surrounding soda soils (ss) from the extremely saline and alkaline lakes of the wadi el natrun in the libyan desert, egypt, were obtained in october 2000. anaerobic enrichment cultures were grown from these samples, dna isolated, and the bacterial diversity assessed by 16s rrna gene clone analysis. clones derived from lake sediments (ls) most closely matched clostridium spp., natronoincola histidinovorans, halocella cellulolytica, bacillus spp., and the cytophaga-flexiba ... | 2004 | 15480866 |
| novel sulfonolipid in the extremely halophilic bacterium salinibacter ruber. | salinibacter ruber is an extremely halophilic bacterium, phylogenetically affiliated with the flavobacterium/cytophaga branch of the domain bacteria. electrospray mass analyses (negative ion) of the total lipid extract of a pure culture of s. ruber shows a characteristic peak at m/z 660 as the most prominent peak in the high-mass range of the spectrum. a novel sulfonolipid, giving rise to the molecular ion [m-h]- of m/z 660, has been identified. the sulfonolipid isolated and purified by thin-lay ... | 2004 | 15528534 |
| influence of an oyster reef on development of the microbial heterotrophic community of an estuarine biofilm. | we characterized microbial biofilm communities developed over two very closely located but distinct benthic habitats in the pensacola bay estuary using two complementary cultivation-independent molecular techniques. biofilms were grown for 7 days on glass slides held in racks 10 to 15 cm over an oyster reef and an adjacent muddy sand bottom. total biomass and optical densities of dried biofilms showed dramatic differences for oyster reef versus non-oyster reef biofilms. this study assessed wheth ... | 2004 | 15528551 |
| soil microbial counts and identification of culturable bacteria in an extreme by arid zone. | sixteen samples of two soil cores (about 550 and 180 cm in depth) were drilled at intervals in the lower reach of heihe river basin (northwest of china) in order to illustrate soil microbial characteristics and diversity of culturable bacteria in an extreme by arid environment. soil water content, organic matter, total nitrogen, ph, direct cell counts, and culturable microorganism counts were evaluated. the total cell concentration was 19-1120/microg (i.e. 0.19-11.2 x 10(8) per g) soil, the cult ... | 2004 | 15530008 |
| 16s rdna library-based analysis of ruminal bacterial diversity. | bacterial 16s rdna sequence data, incorporating sequences > 1 kb, were retrieved from published rumen library studies and public databases, then were combined and analysed to assess the diversity of the rumen microbial ecosystem as indicated by the pooled data. low g+c gram positive bacteria (54%) and the cytophaga-flexibacter-bacteroides (40%) phyla were most abundantly represented. the diversity inferred by combining the datasets was much wider than inferred by individual studies, most likely ... | 2004 | 15539930 |
| aquiflexum balticum gen. nov., sp. nov., a novel marine bacterium of the cytophaga-flavobacterium-bacteroides group isolated from surface water of the central baltic sea. | a bacterial isolate from the baltic sea, ba160(t), was characterized for its physiological and biochemical features, fatty acid profile, g+c content and phylogenetic position based on 16s rrna gene sequences. the strain was isolated from the surface water of the central baltic sea during the decay of a plankton bloom. phylogenetic analyses of the 16s rrna gene sequence revealed a clear affiliation with the family 'flexibacteraceae', and showed the closest phylogenetic relationship with the speci ... | 2004 | 15545480 |
| biological soil crusts of sand dunes in cape cod national seashore, massachusetts, usa. | biological soil crusts cover hundreds of hectares of sand dunes at the northern tip of cape cod national seashore (massachusetts, usa). although the presence of crusts in this habitat has long been recognized, neither the organisms nor their ecological roles have been described. in this study, we report on the microbial community composition of crusts from this region and describe several of their physical and chemical attributes that bear on their environmental role. microscopic and molecular a ... | 2004 | 15546040 |
| analysis and comparison of the microbial community structures of two enrichment cultures capable of reductively dechlorinating tce and cis-dce. | in order to study the effect of different chloroethenes (electron acceptors) on the bacterial composition of dechlorinating communities, two reductive dechlorinating enrichment cultures were developed that were able to reduce trichloroethene (tce) and cis-1,2-dichloroethene (cis-dce) to ethene using hydrogen as electron donor, respectively. the inoculum for the cultures was material from a methanogenic fluidized bed reactor (fbr), which was originally seeded with digester sludge and showed a sta ... | 2004 | 14686940 |
| characterisation of the microbial diversity in a pig manure storage pit using small subunit rdna sequence analysis. | the microbial community structure of pig manure slurry (pms) was determined with comparative analysis of 202 bacterial, 44 archaeal and 33 eukaryotic small subunit (ssu) rdna partial sequences. based on a criterion of 97% of sequence similarity, the phylogenetic analyses revealed a total of 108, eight and five phylotypes for the bacteria, archaea and eukarya lineages, respectively. only 36% of the bacterial phylotypes were closely related (>or=97% similarity) to any previously known sequence in ... | 2004 | 16329909 |
| hydrocarbon contamination changes the bacterial diversity of soil from around scott base, antarctica. | a combination of culture-independent and culturing methods was used to determine the impacts of hydrocarbon contamination on the diversity of bacterial communities in coastal soil from ross island, antarctica. while numbers of culturable aerobic heterotrophic microbes were 1-2 orders of magnitude higher in the hydrocarbon-contaminated soil than control soil, the populations were less diverse. members of the divisions fibrobacter/acidobacterium, cytophaga/flavobacterium/bacteroides, deinococcus/t ... | 2004 | 16329936 |
| belliella baltica gen. nov., sp. nov., a novel marine bacterium of the cytophaga-flavobacterium-bacteroides group isolated from surface water of the central baltic sea. | two bacterial isolates from the baltic sea, ba1 and ba134t, were characterized for their physiological and biochemical features, fatty acid profiles and phylogenetic position based on 16s rrna gene sequences. the strains were isolated from surface water of the central baltic sea during the decay of a plankton bloom. phylogenetic analysis of their 16s rrna gene sequences revealed a clear affiliation to the family 'flexibacteriaceae' and showed highest sequence similarity (91%) to cyclobacterium m ... | 2004 | 14742460 |
| hongiella mannitolivorans gen. nov., sp. nov., hongiella halophila sp. nov. and hongiella ornithinivorans sp. nov., isolated from tidal flat sediment. | three marine strains of the cytophaga-flavobacterium-bacteroides group, designated jc2050t, jc2051t and jc2052t, were obtained from a single sediment sample of getbol, the korean tidal flat. comparative 16s rdna sequence studies revealed that the test strains were not closely related to any validly published genera and that these strains were only distantly related to the genus cyclobacterium (88.7-91.2%). phylogenetic analyses demonstrated that the three getbol isolates formed a distinct monoph ... | 2004 | 14742474 |
| monitoring of bacterial community in a coniferous forest soil after a wildfire. | changes in the soil bacterial community of a coniferous forest were analyzed to assess microbial responses to wildfire. soil samples were collected from three different depths in lightly and severely burned areas, as well as a nearby unburned control area. direct bacterial counts ranged from 3.3-22.6 x 10(8) cells/(g.soil). in surface soil, direct bacterial counts of unburned soil exhibited a great degree of fluctuation. those in lightly burned soil changed less, but no significant variation was ... | 2004 | 15650683 |
| monitoring of soil bacterial community and some inoculated bacteria after prescribed fire in microcosm. | the soil bacterial community and some inoculated bacteria were monitored to assess the microbial responses to prescribed fire in their microcosm. an acridine orange direct count of the bacteria in the unburned control soil were maintained at a relatively stable level (2.0 approximately 2.7 x 10(9) cells/g(-1).soil) during the 180 day study period. the number of bacteria in the surface soil was decreased by fire, but was restored after 3 months. inoculation of some bacteria increased the number o ... | 2004 | 15650684 |
| phylogenetic and physiological diversity of microorganisms isolated from a deep greenland glacier ice core. | we studied a sample from the gisp 2 (greenland ice sheet project) ice core to determine the diversity and survival of microorganisms trapped in the ice at least 120,000 years ago. previously, we examined the phylogenetic relationships among 16s ribosomal dna (rdna) sequences in a clone library obtained by pcr amplification from genomic dna extracted from anaerobic enrichments. here we report the isolation of nearly 800 aerobic organisms that were grouped by morphology and amplified rdna restrict ... | 2004 | 14711643 |
| census of the bacterial community of the gypsy moth larval midgut by using culturing and culture-independent methods. | little is known about bacteria associated with lepidoptera, the large group of mostly phytophagous insects comprising the moths and butterflies. we inventoried the larval midgut bacteria of a polyphagous foliivore, the gypsy moth (lymantria dispar l.), whose gut is highly alkaline, by using traditional culturing and culture-independent methods. we also examined the effects of diet on microbial composition. analysis of individual third-instar larvae revealed a high degree of similarity of microbi ... | 2004 | 14711655 |
| bacterial activity at -2 to -20 degrees c in arctic wintertime sea ice. | arctic wintertime sea-ice cores, characterized by a temperature gradient of -2 to -20 degrees c, were investigated to better understand constraints on bacterial abundance, activity, and diversity at subzero temperatures. with the fluorescent stains 4',6'-diamidino-2-phenylindole 2hcl (dapi) (for dna) and 5-cyano-2,3-ditoyl tetrazolium chloride (ctc) (for o(2)-based respiration), the abundances of total, particle-associated (>3- micro m), free-living, and actively respiring bacteria were determin ... | 2004 | 14711687 |
| development of genetic techniques for the psychrotrophic fish pathogen flavobacterium psychrophilum. | flavobacterium psychrophilum, a member of the cytophaga-flavobacterium-bacteroides group, is an important pathogen of salmonid fish. previous attempts to develop genetic techniques for this fastidious, psychrotrophic bacterium have met with failure. here we describe the development of techniques for the genetic manipulation of f. psychrophilum and the identification of plasmids, selectable markers, a reporter system, and a transposon that function in several isolates of this fish pathogen. the a ... | 2004 | 14711690 |
| intracellular symbionts and other bacteria associated with deer ticks (ixodes scapularis) from nantucket and wellfleet, cape cod, massachusetts. | the diversity of bacteria associated with the deer tick (ixodes scapularis) was assessed using pcr amplification, cloning, and sequencing of 16s rrna genes originating from seven ticks collected from nantucket island and wellfleet, cape cod, mass. the majority of sequences obtained originated from gram-negative proteobacteria. four intracellular bacteria were detected including strains of ehrlichia, rickettsia, and wolbachia and an organism related to intracellular insect symbionts from the cyto ... | 2004 | 14711698 |
| genomics of the cconoqp-encoded cbb3 oxidase complex in bacteria. | many bacteria adapt to microoxic conditions by synthesizing a particular cytochrome c oxidase (cbb3) complex with a high affinity for o2, encoded by the cconoqp operon. a survey of genome databases indicates that cconoqp sequences are widespread in all sub-branches of proteobacteria but otherwise are found only in bacteria of the cfb group ( cytophaga, flexibacter, bacteroides). our analysis of available genome sequences suggests four major strategies of regulating cconoqp expression in response ... | 2004 | 14714103 |
| distribution of two triamines, spermidine and homospermidine, and an aromatic amine, 2-phenylethylamine, within the phylum bacteroidetes. | cellular polyamines of the newly additional 19 species belonging to the class bacteroides of the phylum bacteroidetes were analyzed by hplc to display polyamine distribution as a chemotaxonomic marker within the total 41 species. three profiles, the presence of spermidine, the presence of homospermidine and the absence of both triamines, corresponded to their phylogenetical positions within the four families of the class. the occurrence of an aromatic amine, 2-phenylethylamine, extracted into ce ... | 2004 | 15747230 |
| performances and microbial features of a granular activated carbon packed-bed biofilm reactor capable of an efficient anaerobic digestion of olive mill wastewaters. | anaerobic digestion of olive mill wastewaters is generally performed in anaerobic contact bioreactors where the removal of toxic phenols is often unsatisfactory. in the present work we show that a granular activated carbon packed-bed biofilm reactor can be successfully used to achieve effective and reproducible wastewater decontamination even at high organic loads. a comparison of 16s rrna gene sequences of the inoculum and of biomass samples from different districts of the reactor revealed enri ... | 2004 | 19712310 |
| phylogenetic diversity of bacteria associated with paleolithic paintings and surrounding rock walls in two spanish caves (llonín and la garma). | bacterial diversity in caves is still rarely investigated using culture-independent techniques. in the present study, bacterial communities on paleolithic paintings and surrounding rock walls in two spanish caves (llonín and la garma) were analyzed, using 16s rdna-based denaturing gradient gel electrophoresis community fingerprinting and phylogenetic analyses without prior cultivation. results revealed complex bacterial communities consisting of a high number of novel 16s rdna sequence types and ... | 2004 | 19712338 |
| phylogenetic diversity of bacteria in the leachate of a full-scale recirculating landfill. | we analyzed the phylogenetic composition of bacterial community in the effluent leachate of a full-scale recirculating landfill using a culture-independent molecular approach. 16s rrna genes were amplified directly from leachate dna with universally conserved and bacteria-specific rdna primers and cloned. the clone library was screened by restriction fragment length polymorphism, and representative rdna sequences were determined. many bacterial sequences displaying relatively low levels of simil ... | 2004 | 19712358 |
| identification of rice root associated nitrate, sulfate and ferric iron reducing bacteria during root decomposition. | leakage of o(2) from roots of aquatic plants supports the oxidation of ammonia to nitrate and of sulfide to sulfate in the rhizosphere, so that these electron acceptors may become available to the root microbial communities and affect their activity. we studied the composition of the bacterial community active in anoxically incubated rice roots by analysis of terminal restriction fragment length polymorphism (t-rflp) and by cloning and sequencing targeting bacterial 16s rrna. the bacterial ribos ... | 2004 | 19712368 |
| distribution of prokaryotic genetic diversity in athalassohaline lakes of the atacama desert, northern chile. | athalassohaline lakes are inland saline aquatic environments with ionic proportions quite different from the dissolved salts in seawater. prokaryotes inhabiting athalassohaline environments are poorly known and very few of such places have been surveyed for microbial diversity studies around the world. we analyzed the planktonic bacterial and archaeal assemblages inhabiting several of these evaporitic basins in a remote and vast area in northern chile by pcr-denaturing gradient gel electrophores ... | 2004 | 19712431 |
| the modular xylanase xyn10a from rhodothermus marinus is cell-attached, and its c-terminal domain has several putative homologues among cell-attached proteins within the phylum bacteroidetes. | until recently, the function of the fifth domain of the thermostable modular xylanase xyn10a from rhodothermus marinus was unresolved. a putative homologue to this domain was however identified in a mannanase (man26a) from the same microorganism which raised questions regarding a common function. an extensive search of all accessible data-bases as well as the partially sequenced genomes of r. marinus and cytophaga hutchinsonii showed that homologues of this domain were encoded by multiple genes ... | 2004 | 15598538 |
| bacterial population association with phytoplankton cultured in a bivalve hatchery. | bacterial populations association with phytoplankton cultures used as food for bivalve larvae were enumerated and identified from their partial 16s rdna gene sequences. microalgae were provided from different european hatcheries during the larval production season. average concentration (direct counts) of bacteria ranged from 1.3 x 10(5) to 5.3 x 10(8) ml(-1) while culturable bacteria represented from 10% to >60% of total bacteria. in most cases, three to six representatives of each type of colo ... | 2004 | 15692860 |
| a shallow btex and mtbe contaminated aquifer supports a diverse microbial community. | microbial communities in subsurface environments are poorly characterized and the impacts of anthropogenic contamination on their structure and function have not been adequately addressed. the release of contaminant(s) to a previously unexposed environment is often hypothesized to decrease the diversity of the affected community. we characterized the structure of microbial communities along a gradient of benzene, toluene, ethylbenzene, and xylene (btex) and methyl-tert-butyl-ether (mtbe) contami ... | 2004 | 15696392 |
| microbial community analysis and performance of a phosphate-removing activated sludge. | the microbial community of a phosphate-removing activated sludge was analyzed according to the extracted 16s rdna sequences. the sludge, which accumulated 5.6% p by weight, was obtained from a sequencing batch reactor treating a fatty-acid rich wastewater containing 108 mg l(-1) total organic carbon (toc), 14.0 mg l(-1) n and 16.2 mg l(-1) p. the reactor at 25 degrees c and ph 7.6 removed over 96% toc and 99.9% p from the wastewater. according to the 16s rdna analysis of the 114 clones developed ... | 2005 | 15734306 |
| molecular phylogenetic diversity of bacteria associated with the leachate of a closed municipal solid waste landfill. | a 16s rdna-based molecular study was performed to determine the nature of the bacterial constituents of the leachate from a closed municipal solid waste landfill. total community dna was extracted and bacterial 16s rrna genes were subsequently amplified and cloned. recombinant rdna clones in the library were randomly selected, and they were sequenced for a single run and then grouped. a total of 76 sequence types representing 138 randomly selected nonchimeric clones were identified. full-length ... | 2005 | 15621451 |
| [phylogenetic diversity analyse of rumen bacteria using culture independent method]. | culture independent method was used to study the diversity of rumen bacteria. molecular diversity of rumen bacteria was analyzed by pcr amplification and sequencing of 16s rdna clone libraries prepared from the rumen content of holstein cows. the total dna directly extracted from rumen fluid was used as pcr template. bacteria universal primer 27f and 1492r was used as primer. random clones, containing almost full size 16s rdna sequences (about 1.5 kb long), were sequenced and subjected to an on ... | 2005 | 16496703 |
| volatile organic compounds from arctic bacteria of the cytophaga-flavobacterium-bacteroides group: a retrobiosynthetic approach in chemotaxonomic investigations. | volatile organic compounds emitted by different marine arctic strains of the cytophaga-flavobacterium-bacteroides group were investigated by using a modified closed-loop stripping apparatus (clsa). seven of nine strains emitted volatiles, dominated by methyl ketones, in specific patterns. the methyl ketones were aliphatic saturated, or unsaturated, and comprised 12 to 18 c-atoms, sometimes with terminal me branches. they were identified by gc/ms, retention-index calculations, derivatization with ... | 2005 | 17191983 |
| polysaccharide-producing bacteria isolated from paper machine slime deposits. | development of novel enzymatic methods for slime deposit control in paper mills requires knowledge of polysaccharide-producing organisms and the polysaccharide structures present in deposits. in this work, 27 polysaccharide-producing bacteria were isolated from slime samples collected from different parts of a paper machine. most of the isolates produced polysaccharides in liquid culture and nine of them were selected for production of polysaccharides for characterisation. the selected isolates ... | 2005 | 15750806 |
| evaluation of candidate probiotic strains for gilthead sea bream larvae (sparus aurata) using an in vivo approach. | the aim of this study was to evaluate the effect of six bacterial strains on gilthead sea bream larvae (sparus aurata). | 2005 | 15752217 |
| the diversity of culturable organotrophic bacteria from local solar salterns. | we isolated and cultured bacteria inhabiting solar saltern ponds in taean-gun, chungnam province, korea. all of the isolated 64 strains were found to be moderately halophilic bacteria, growing in a salt range of 2-20 %, with an optimal concentration of 5% salt. bacterial diversity among the isolated halophiles was evaluated via rflp analyses of pcr-amplified 16s rdnas, followed by phylogenetic analysis of the partial 16s rdna sequences. the combination of restriction enzyme digestions with haeii ... | 2005 | 15765050 |
| [hydrolytic activity of marine bacteria associated with the mussel mytilus trossulus]. | the ability to produce hydrolytic enzymes--dnases, rnases, alkaline phosphatases, chitinases has been studied in 316 strains of bacteria isolated from mussel mytilus trossulus. strains of vibrio spp. produced all the spectrum of examined enzymes, bacteria of pseudoalteromonas genus produced alkaline phosphatase and dnase. chitin-degrading enzymes were found in vibrio and cytophaga--flavobacterium--bacteroides group. bacillus and vibrio spp. strains produced most actively rnases. the presence of ... | 2005 | 15765877 |
| adhaeribacter aquaticus gen. nov., sp. nov., a gram-negative isolate from a potable water biofilm. | a gram-negative bacterium was isolated from a freshwater biofilm developed on a stainless steel surface under a fluid velocity of 0.26 m s(-1). the strain, mbrg1.5(t), was cultivated on r2a agar and formed pink colonies. light microscopy and negative staining in a transmission electron microscope showed that the cells were rod-shaped, approximately 2.8-4.1 microm long by 0.9-1.7 microm wide in size and produced large quantities of extracellular fibrillar material. additionally, following growth ... | 2005 | 15774669 |
| marinicola seohaensis gen. nov., sp. nov., isolated from sea water of the yellow sea, korea. | a gram-negative, non-flagellated, non-spore-forming and rod-shaped bacterial strain, sw-152(t), was isolated from sea water of the yellow sea in korea, and subjected to a polyphasic taxonomic study. strain sw-152(t) grew optimally at 30 degrees c and in the presence of 2-3 % (w/v) nacl. it contained mk-7 as the predominant menaquinone and iso-c(15 : 0) and iso-c(15 : 1) as the major fatty acids. polar lipids detected in strain sw-152(t) were phosphatidylethanolamine, diphosphatidylglycerol and u ... | 2005 | 15774675 |
| incorporation of glucose under anoxic conditions by bacterioplankton from coastal north sea surface waters. | it has been hypothesized that the potential for anaerobic metabolism might be a common feature of bacteria in coastal marine waters (l. riemann and f. azam, appl. environ. microbiol. 68: 5554-5562, 2002). therefore, we investigated whether different phylogenetic groups of heterotrophic picoplankton from the coastal north sea were able to take up a simple carbon source under anoxic conditions. oxic and anoxic incubations (4 h) or enrichments (24 h) of seawater with radiolabeled glucose were perfo ... | 2005 | 15811993 |
| reclassification of [cytophaga] marinoflava reichenbach 1989 as leeuwenhoekiella marinoflava gen. nov., comb. nov. and description of leeuwenhoekiella aequorea sp. nov. | five heterotrophic, aerobic, halotolerant and pigmented bacterial strains with gliding motility were isolated from antarctic sea water; one other isolate was collected from the sea urchin strongylocentrotus intermedius in the gulf of peter the great in the sea of japan. 16s rrna gene sequence analysis indicated that the strains are members of the family flavobacteriaceae, the nearest neighbour (with 97.1 % sequence similarity) being the misclassified species [cytophaga] marinoflava. dna-dna hybr ... | 2005 | 15879230 |
| microbial adaptation to biodegradation of tert-butyl alcohol in a sequencing batch reactor. | this study demonstrates the utility of the sequencing batch reactor (sbr) to adapt microorganisms towards biological removal of tert-butyl alcohol (tba). the reactor was inoculated with activated sludge and fed with tba as the sole carbon source. start-of-cycle tba concentrations were initially set at 100 mgl(-1) with a cycle time of 24 h and a volumetric exchange ratio of 50% to maintain a tba loading rate of not more than 100 mgl(-1)d(-1). step increases in tba loading rates up to 600 mgl(-1)d ... | 2005 | 15899532 |
| a molecular systematic survey of cultured microbial associates of deep-water marine invertebrates. | a taxonomic survey was conducted to determine the microbial diversity held within the harbor branch oceanographic marine microbial culture collection (hbmmcc). the collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. a total of 2273 heterotrophic bacterial isolates were inventoried using the dna fingerprinting technique amplified rdna restriction analysis on approximately 750-800 base pairs (bp) encompassing hypervariable regio ... | 2005 | 15900971 |
| identification and characterization of potentially algal-lytic marine bacteria strongly associated with the toxic dinoflagellate alexandrium catenella. | the toxic dinoflagellate alexandrium catenella isolated from fjords in southern chile produces several analogues of saxitoxin and has been associated with outbreaks of paralytic shellfish poisoning. three bacterial strains, which remained in close association with this dinoflagellate in culture, were isolated by inoculating the dinoflagellate onto marine agar. the phenotypically different cultivable bacterial colonies were purified. their genetic identification was done by polymerase chain react ... | 2005 | 15926994 |
| isolation and identification of freshwater bacteria antagonistic to giardia intestinalis cysts. | we have isolated three freshwater bacterial strains that demonstrate the ability to degrade giardia intestinalis cysts. these strains have been identified by 16s rrna sequencing and phylogenetic analysis as belonging to the flavobacterium columnare clade of the cytophaga-flavobacterium group. while the cyst degradation mechanism is unclear, two different effects on the cysts were observed: non-viability and lysis. cysts exposed to bacterial strains br1 and sc1 were generally non-viable, but rema ... | 2005 | 15952456 |
| bacterial diversity and carbonate precipitation in the giant microbialites from the highly alkaline lake van, turkey. | lake van harbors the largest known microbialites on earth. the surface of these huge carbonate pinnacles is covered by coccoid cyanobacteria whereas their central axis is occupied by a channel through which neutral, relatively ca-enriched, groundwater flows into highly alkaline (ph approximately 9.7) ca-poor lake water. previous microscopy observations showed the presence of aragonite globules composed by rounded nanostructures of uncertain origin that resemble similar bodies found in some meteo ... | 2005 | 15959626 |
| fate of 14c-labeled microbial products derived from nitrifying bacteria in autotrophic nitrifying biofilms. | the cross-feeding of microbial products derived from 14c-labeled nitrifying bacteria to heterotrophic bacteria coexisting in an autotrophic nitrifying biofilm was quantitatively analyzed by using microautoradiography combined with fluorescence in situ hybridization (mar-fish). after only nitrifying bacteria were labeled with [14c]bicarbonate, biofilm samples were incubated with and without nh4+ as a sole energy source for 10 days. the transfer of 14c originally incorporated into nitrifying bacte ... | 2005 | 16000813 |
| molecular assessment of inoculated and indigenous bacteria in biofilms from a pilot-scale perchlorate-reducing bioreactor. | bioremediation of perchlorate-contaminated groundwater can occur via bacterial reduction of perchlorate to chloride. although perchlorate reduction has been demonstrated in bacterial pure cultures, little is known about the efficacy of using perchlorate-reducing bacteria as inoculants for bioremediation in the field. a pilot-scale, fixed-bed bioreactor containing plastic support medium was used to treat perchlorate-contaminated groundwater at a site in southern california. the bioreactor was ino ... | 2005 | 16003477 |
| changes in the rrna levels of specific microbial groups in activated sludge during sample handling and storage. | to quantitatively analyse the changes in group-specific rrna levels in activated sludge as a function of sample handling and storage procedure. | 2005 | 16033523 |
| chemical characterization of exopolysaccharides from antarctic marine bacteria. | exopolysaccharides (eps) may have an important role in the antarctic marine environment, possibly acting as ligands for trace metal nutrients such as iron or providing cryoprotection for growth at low temperature and high salinity. ten bacterial strains, isolated from southern ocean particulate material or from sea ice, were characterized. whole cell fatty acid profiles and 16s rrna gene sequences showed that the isolates included representatives of the genera pseudoalteromonas, shewanella, pola ... | 2005 | 16052372 |
| effects of bacteria on artemia franciscana cultured in different gnotobiotic environments. | the use of probiotics is receiving considerable attention as an alternative approach to control microbiota in aquaculture farms, especially in hatching facilities. however, application with consistent results is hampered by insufficient information on their modes of action. to investigate whether dead bacteria (allowing investigation of their nutritional effect) or live bacteria (allowing evaluation of their probiotic effect) have any beneficial effect towards artemia franciscana and, subsequent ... | 2005 | 16085818 |
| responses of baltic sea ice and open-water natural bacterial communities to salinity change. | to investigate the responses of baltic sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. bacterial communities of baltic seawater and sea ice from a coastal site in southwest finland were used in two batch culture experiments run for 17 or 18 days at 0 degrees c. bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. the bacterial community structure was asses ... | 2005 | 16085826 |
| 16s rrna sequences and differences in bacteria isolated from the muztag ata glacier at increasing depths. | small subunit 16s rrna sequences, growth temperatures, and phylogenetic relationships have been established for 129 bacterial isolates recovered under aerobic growth conditions from different regions of a 22-m ice core from the muztag ata mountain glacier on the pamirs plateau (china). only 11% were psychrophiles (grew at 2 degrees c or -2 degrees c up to approximately 20 degrees c), although the majority (82%) were psychrotolerant (grew at 2 degrees c or -2 degrees c up to 37 degrees c). the ma ... | 2005 | 16085856 |
| "bacteroides goldsteinii sp. nov." isolated from clinical specimens of human intestinal origin. | phenotypic and phylogenetic studies were performed on an unknown gram-negative, strictly anaerobic, rod-shaped bacterium isolated from human clinical specimens. this organism was indole negative, resistant to 20% bile, produced acetic and a lesser amount of succinic acids as the major end products of glucose metabolism, and possessed a g+c content of approximately 43 mol%. comparative 16s rrna gene sequencing demonstrated that the unidentified bacterium was a member of the cytophaga-flavobacter- ... | 2005 | 16145101 |
| resistance of marine bacterioneuston to solar radiation. | a total of 90 bacterial strains were isolated from the sea surface microlayer (i.e., bacterioneuston) and underlying waters (i.e., bacterioplankton) from two sites of the northwestern mediterranean sea. the strains were identified by sequence analysis, and growth recovery was investigated after exposure to simulated solar radiation. bacterioneuston and bacterioplankton isolates were subjected to six different exposure times, ranging from 0.5 to 7 h of simulated noontime solar radiation. followin ... | 2005 | 16151115 |
| rrna sequence-based scanning electron microscopic detection of bacteria. | a new scanning electron microscopic method was developed for gaining both phylogenetic and morphological information about target microbes using in situ hybridization with rrna-targeted oligonucleotide probes (sem-ish). target cells were hybridized with oligonucleotide probes after gold labeling. gold enhancement was used for amplification of probe signals from hybridized cells. the hybridized cells released a strong backscatter electron signal due to accumulation of gold atoms inside cells. sem ... | 2005 | 16151145 |
| specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. | high-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. a total of 570 bacterial cultures were obtained by employing the most probable number and microdrop techniques. the majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the alpha-proteobacteria, beta-proteobacteria, actinobacteria, firmicutes, or flavobacteria-c ... | 2005 | 16204504 |
| culturable bacterial symbionts isolated from two distinct sponge species (pseudoceratina clavata and rhabdastrella globostellata) from the great barrier reef display similar phylogenetic diversity. | the diversity of the culturable microbial communities was examined in two sponge species-pseudoceratina clavata and rhabdastrella globostellata. isolates were characterized by 16s rrna gene sequencing and phylogenetic analysis. the bacterial community structures represented in both sponges were found to be similar at the phylum level by the same four phyla in this study and also at a finer scale at the species level in both firmicutes and alphaproteobacteria. the majority of the alphaproteobacte ... | 2005 | 16215644 |
| description of aquimarina muelleri gen. nov., sp. nov., and proposal of the reclassification of [cytophaga] latercula lewin 1969 as stanierella latercula gen. nov., comb. nov. | the taxonomic position of three novel sea-water isolates was determined. the strains studied were strictly aerobic, heterotrophic, pigmented, motile by gliding, gram-negative and oxidase-, catalase-, beta-galactosidase- and alkaline phosphatase-positive. 16s rrna gene sequence phylogenetic analysis indicated that the strains kmm 6020t, kmm 6021 and kmm 6028 occupied a distinct lineage within the family flavobacteriaceae. the major respiratory quinone was mk-6. the predominant fatty acids were i1 ... | 2005 | 15653878 |
| the microbial community structure of different permeable sandy sediments characterized by the investigation of bacterial fatty acids and fluorescence in situ hybridization. | this study describes the microbial community structure of three sandy sediment stations that differed with respect to median grain size and permeability in the german bight of the southern north sea. the microbial community was investigated using lipid biomarker analyses and fluorescence in situ hybridization. for further characterization we determined the stable carbon isotope composition of the biomarkers. biomarkers identified belong to different bacterial groups such as members of the cytoph ... | 2005 | 15658995 |
| characterization of the roka and hexa broad-substrate-specificity hexokinases from bacteroides fragilis and their role in hexose and n-acetylglucosamine utilization. | bacteroides fragilis, a human gastrointestinal commensal and an opportunistic pathogen, utilizes simple and complex sugars and polysaccharides for growth in the large intestine and at sites of infection. because b. fragilis lacks transport-linked sugar phosphorylation systems, cytoplasmic kinase(s) was expected to be required for the phosphorylation of hexoses and hexosamines. we have now identified two hexose kinases that are important for growth of b. fragilis on glucose, mannose, and other su ... | 2005 | 15659667 |
| links between phytoplankton and bacterial community dynamics in a coastal marine environment. | bacteria and phytoplankton dynamics are thought to be closely linked in coastal marine environments, with correlations frequently observed between bacterial and phytoplankton biomass. in contrast, little is known about how these communities interact with each other at the species composition level. the purpose of the current study was to analyze bacterial community dynamics in a productive, coastal ecosystem and to determine whether they were related to phytoplankton community dynamics. near-sur ... | 2005 | 15688258 |
| structure of sediment-associated microbial communities along a heavy-metal contamination gradient in the marine environment. | microbial community composition and structure were characterized in marine sediments contaminated for >80 years with cadmium, copper, lead, and zinc. four sampling sites that encompass a wide range of sediment metal loads were compared in a norwegian fjord (sorfjord). hcl-extractable metals and organic matter constantly decreased from the most contaminated site (s1) to the control site (s4). all sampling sites presented low polychlorinated biphenyl (pcb) concentrations (sigma(7)pcb < 7.0 ng g [d ... | 2005 | 15691917 |
| assimilation of polysaccharides and glucose by major bacterial groups in the delaware estuary. | the contribution of major bacterial groups to the assimilation of extracellular polymeric substances (eps) and glucose in the delaware estuary was assessed using microautoradiography and fluorescence in situ hybridization. bacterial groups contributed to eps and glucose assimilation in part according to their distribution in the estuary. abundance of the phylogenetic groups explained 35% and 55% of the variation in eps and glucose assimilation, respectively. actinobacteria contributed 70% to glu ... | 2005 | 16332754 |
| detection and isolation of ultrasmall microorganisms from a 120,000-year-old greenland glacier ice core. | the abundant microbial population in a 3,043-m-deep greenland glacier ice core was dominated by ultrasmall cells (<0.1 microm3) that may represent intrinsically small organisms or starved, minute forms of normal-sized microbes. in order to examine their diversity and obtain isolates, we enriched for ultrasmall psychrophiles by filtering melted ice through filters with different pore sizes, inoculating anaerobic low-nutrient liquid media, and performing successive rounds of filtrations and recult ... | 2005 | 16332755 |
| chitinase genes in lake sediments of ardley island, antarctica. | a sediment core spanning approximately 1,600 years was collected from a lake on ardley island, antarctica. the sediment core had been greatly influenced by penguin guano. using molecular methods, the chitinolytic bacterial community along the sediment core was studied over its entire length. primers targeting conserved sequences of the catalytic domains of family 18 subgroup a chitinases detected group a chitinases from a wide taxonomic range of bacteria. using quantitative competitive pcr (qc-p ... | 2005 | 16332766 |
| sequence and expression analyses of cytophaga-like hydrolases in a western arctic metagenomic library and the sargasso sea. | sequence analysis of environmental dna promises to provide new insights into the ecology and biogeochemistry of uncultured marine microbes. in this study we used the sargasso sea whole genome sequence (wgs) data set to search for hydrolases used by cytophaga-like bacteria to degrade biopolymers such as polysaccharides and proteins. analysis of the sargasso wgs data for contigs bearing both the 16s rrna genes of cytophaga-like bacteria and hydrolase genes revealed a cellulase gene (celm) most sim ... | 2005 | 16332841 |
| culture-dependent and -independent approaches establish the complexity of a pah-degrading microbial consortium. | a microbial consortium (am) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (pah) mixture of three- and four-ringed pahs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (dgge), and the screening of 16s and 18s rrna gene clone libraries. eleven different sequences by culture-dependent techniques and seven by both dgge and clone libraries wer ... | 2005 | 16333329 |
| bacterial diversity in water samples from uranium wastes as demonstrated by 16s rdna and ribosomal intergenic spacer amplification retrievals. | bacterial diversity was assessed in water samples collected from several uranium mining wastes in ger many and in the united states by using 16s rdna and ribosomal intergenic spacer amplification retrievals. the results obtained using the 16s rdna retrieval showed that the samples collected from the uranium mill tailings of schlema/alberoda, germany, were predominated by nitrospina-like bacteria, whereas those from the mill tailings of shiprock, new mexico, usa, were predominated by gamma-pseudo ... | 2005 | 16333330 |
| molecular characterization of an oil-degrading cyanobacterial consortium. | recent studies have shown that the cyanobacterium microcoleus chthonoplastes forms a consortium with heterotrophic bacteria present within the cyanobacterial sheath. these studies also show that this consortium is able to grow in the presence of crude oil, degrading aliphatic heterocyclic organo-sulfur compounds as well as alkylated monocyclic and polycyclic aromatic hydrocarbons. in this work, we characterize this oil-degrading consortium through the analysis of the 16s rrna gene sequences. we ... | 2005 | 16341637 |
| effects of selected pharmaceuticals on riverine biofilm communities. | although pharmaceutical and therapeutic products are widely found in the natural environment, there is limited understanding of their ecological effects. here we used rotating annular bioreactors to assess the impact of 10 microg.l(-1) of the selected pharmaceuticals ibuprofen, carbamazepine, furosemide, and caffeine on riverine biofilms. after 8 weeks of development, community structure was assessed using in situ microscopic analyses, fluor-conjugated lectin binding, standard plate counts, fluo ... | 2005 | 16234864 |
| growth and grazing mortality rates of phylogenetic groups of bacterioplankton in coastal marine environments. | dilution culture experiments were conducted in western north pacific coastal regions to determine growth and grazing mortality rates of bacterial phylogenetic groups (alpha-, beta-, and gamma-proteobacteria and the cytophaga-flavobacter cluster) detected by fluorescent in situ hybridization. growth rates varied greatly (1.2- to 4.0-fold) among different groups, and they were related to environmental variables (chlorophyll a concentrations and temperature) in a group-specific fashion. growth rate ... | 2005 | 16269712 |
| bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. | bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. the dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (pah) degraders, and the total petroleum hydrocarbon (tph) and pah concentrations were monitored during the bioremediation process. tph and pahs were significantly degraded in all treatments (72 to 79% and 83 to 87%, ... | 2005 | 16269736 |
| proteiniphilum acetatigenes gen. nov., sp. nov., from a uasb reactor treating brewery wastewater. | two proteolytic, strictly anaerobic bacterial strains (tb107(t) and tb6-6) were isolated from the granule sludge of an upflow anaerobic sludge blanket reactor treating brewery wastewater. the strains were gram-negative, non-spore-forming and motile. cells were rod-shaped (0.6-0.9x1.9-2.2 microm). growth of the strains was observed at 20-45 degrees c and ph 6.0-9.7. the strains were proteolytic. yeast extract, peptone, pyruvate, glycine and l-arginine could be used as carbon and energy sources. w ... | 2005 | 16280479 |
| bacterial diversity of metagenomic and pcr libraries from the delaware river. | to determine whether metagenomic libraries sample adequately the dominant bacteria in aquatic environments, we examined the phylogenetic make-up of a large insert metagenomic library constructed with bacterial dna from the delaware river, a polymerase chain reaction (pcr) library of 16s rrna genes, and community structure determined by fluorescence in situ hybridization (fish). the composition of the libraries and community structure determined by fish differed for the major bacterial groups in ... | 2005 | 16309387 |
| extracellular enzyme activity and dynamics of bacterial community in mucilaginous aggregates of the northern adriatic sea. | bacterial degradation of mucilaginous aggregates (creamy layers, stringers and macroflocs) collected during two summer events (2001-2002) was tested. the objective was to describe the temporal trend of the bacterial activity, abundance and composition in the aggregated and dissolved organic matter under different trophic conditions. in the native aggregates proteins and organic phosphorous were actively hydrolyzed as aminopeptidase and alkaline phosphatase activities represented up to 87% and 25 ... | 2005 | 16310835 |
| [characterization of communities of heterotrophic bacteria associated with healthy and diseased corals in nha trang bay (vietnam)]. | a comparative investigation of the heterotrophic microflora of 11 species of healthy corals and of white-band-diseased and yellow-band-diseased corals inhabiting the reefs of nha trang bay (vietnam), which has been exposed to anthropogenic impact, was performed. fifty-nine strains of heterotrophic bacteria isolated on y/k and endo media were investigated and characterized. all the isolates were identified at the genus level by consideration of the results of analysis of their phenotypic properti ... | 2005 | 16315986 |
| fatty acid profiling of microbial community during aging of mucilaginous aggregates in the northern adriatic. | aggregates differing in size and phytoplankton community composition were sampled in winter/spring 2001 and summer 1997 and 2002 (during mucilaginous event) in the northern adriatic sea. the fatty acid profiles (fame) were determined in aggregates, bacterial population was grown from each aggregate and each bacterial isolate from aggregate's plated cultures. all aggregates irrespective of the season, aggregate size or phytoplankton community composition contained isolates from three distinct gro ... | 2005 | 15589252 |
| isolation of poly-3-hydroxybutyrate metabolism genes from complex microbial communities by phenotypic complementation of bacterial mutants. | the goal of this study was to initiate investigation of the genetics of bacterial poly-3-hydroxybutyrate (phb) metabolism at the community level. we constructed metagenome libraries from activated sludge and soil microbial communities in the broad-host-range incp cosmid prk7813. several unique clones were isolated from these libraries by functional heterologous complementation of a sinorhizobium meliloti bdha mutant, which is unable to grow on the phb cycle intermediate d-3-hydroxybutyrate due t ... | 2006 | 16391068 |
| microbial diversity in sediments of saline qinghai lake, china: linking geochemical controls to microbial ecology. | saline lakes at high altitudes represent an important and extreme microbial ecosystem, yet little is known about microbial diversity in such environments. the objective of this study was to examine the change of microbial diversity from the bottom of the lake to sediments of 40 cm in depth in a core from qinghai lake. the lake is saline (12.5 g/l salinity) and alkaline (ph 9.4) and is located on the qinghai-tibetan plateau at an altitude of 3196 m above sea level. pore water chemistry of the cor ... | 2006 | 16400537 |
| bacterial diversity in organically-enriched fish farm sediments. | the bacterial diversity and community structure within both organically enriched and adjacent, unimpacted, near-shore marine sediments at two fish farms in southern tasmania, australia, was examined using 16s rrna gene clone library construction and analysis. sediments at both caged and reference sites at both farms showed a very high level of microbial diversity. over 900 clones were analysed and grouped into 631 unique phylotypes. reference sites were dominated by delta- and gammaproteobacteri ... | 2006 | 16420614 |
| a digital imaging procedure for seven-probe-labeling fish (rainbow-fish) and its application to estuarine microbial communities. | for multi-probe-labeling fluorescence in situ hybridization (fish), a digital imaging procedure was developed consisting of systematic background noise reduction and target signal equalization using a hue, saturation, value color partitioning technique. by the combined application of seven dna probes, each labeled with three fluorochromes at maximum, seven kinds of cultured type strains were distinguished in a microscopic field simultaneously. using this seven-probe-labeling fish (rainbow-fish), ... | 2006 | 16420624 |
| microbial community structure of sandy intertidal sediments in the north sea, sylt-rømø basin, wadden sea. | molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of sylt (wadden sea) at a site which was characterized for transport and mineralization rates in a parallel study (d. de beer, f. wenzhöfer, t. ferdelman, s.e. boehme, m. huettel, j.e.e. van beusekom, m.e. böttcher, n. musat, n. dubilier, transport and mineralization rates in north sea sandy intertidal sediments, sylt-romo basin, wadden sea, limnol. ... | 2006 | 16431068 |
| fluorescent in situ hybridization (fish) for the detection of bacterial community in activated sludge from textile factories. | conventional methods used to study the bacterial community structure in activated sludge are not sufficient enough to determine the compositions of the bacterial populations responsible for biodegradation. activated sludge samples from 3 textile factories were analyzed by fluorescent in situ hybridization (fish) using rrna probes and by phase-contrast microscopy. in factory-i, the predominant groups were the beta-subclass of proteobacteria and the cytophaga-flavobacterium (cf) cluster (33.3% and ... | 2006 | 16457176 |
| vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the florida escarpment. | the bacterial and archaeal communities of the sediments at the base of the florida escarpment (gulf of mexico, usa) were investigated using molecular phylogenetic analysis. the total microbial community dna of each of three vertical zones (top, middle and bottom) of a sediment core was extracted and the 16s rrna genes were amplified by pcr, cloned and sequenced. shannon-weaver diversity measures of bacteria were high in all three zones. for the archaea, diversity was generally low, but increased ... | 2006 | 16465452 |
| microbial communities and fecal indicator bacteria associated with cladophora mats on beach sites along lake michigan shores. | a high biomasses of cladophora, a filamentous green alga, is found mainly during the summer along the shores of lake michigan. in this study, the abundance and persistence of the fecal indicator bacterium escherichia coli and sulfate-reducing bacteria (srb) on cladophora mats collected at lake michigan beaches were evaluated using both culture-based and molecular analyses. additionally, 16s rrna gene cloning and sequencing were used to examine the bacterial community composition. overall, e. col ... | 2006 | 16517640 |
| in vitro cultivation and antibiotic susceptibility of a cytophaga-like intracellular symbiote isolated from the tick ixodes scapularis. | a cytophaga-like organism (clo), isolated from the tick ixodes scapularis (isclo), was adapted to growth in insect cell lines and its antibiotic sensitivity was tested. isclo were introduced to four insect cell lines, and their growth was measured by quantitative polymerase chain reaction. isclo propagated well in a mosquito cell line, aeal-2, and caused cytopathic effects in host cells. a lepidopteran cell line, hz-am1, was also suitable for propagation of isclo and kept a steady state with bac ... | 2006 | 16550461 |
| identification of bacterial diversity in the oyster crassostrea gigas by fluorescent in situ hybridization and polymerase chain reaction. | to carry out a rapid and reliable identification of bacterial diversity in the oyster crassostrea gigas from todos santos bay, méxico, in the current study we applied the molecular techniques of fluorescent in situ hybridization (fish) and polymerase chain reaction (pcr). in order to reach this goal, genus and group-specific oligonucleotides targeted to 16s rdna/rrna were used. | 2006 | 16553721 |
| characterization of psychrotolerant heterotrophic bacteria from finnish lapland. | a total of 331 aerobic heterotrophic bacterial strains were isolated from various ecosystems of finnish lapland (68-69 degrees n) including forest soil, arctic alpine-tundra soil, stream water, lake and mire sediments, lichen and snow algae. whole cell fatty acid and 16s rrna gene sequence analysis and microscopy indicated that the isolates were dominated by gram-negative bacteria, while only 20 gram-positive strains were isolated. based on 16s rrna gene sequences the isolates were members of al ... | 2006 | 16564959 |
| acetylornithine transcarbamylase: a novel enzyme in arginine biosynthesis. | ornithine transcarbamylase is a highly conserved enzyme in arginine biosynthesis and the urea cycle. in xanthomonas campestris, the protein annotated as ornithine transcarbamylase, and encoded by the argf gene, is unable to synthesize citrulline directly from ornithine. we cloned and overexpressed this x. campestris gene in escherichia coli and show that it catalyzes the formation of n-acetyl-l-citrulline from n-acetyl-l-ornithine and carbamyl phosphate. we now designate this enzyme as an acetyl ... | 2006 | 16585758 |
| a mutation in flavobacterium psychrophilum tlpb inhibits gliding motility and induces biofilm formation. | flavobacterium psychrophilum is a psychrotrophic, fish-pathogenic bacterium belonging to the cytophaga-flavobacterium-bacteroides group. tn4351-induced mutants deficient in gliding motility, growth on iron-depleted media, and extracellular proteolytic activity were isolated. some of these mutants were affected in only one of these characteristics, whereas others had defects in two or more. fp523, a mutant deficient in all of these properties, was studied further. fp523 had a tn4351 insertion in ... | 2006 | 16751514 |
| incorporation of 3h-thymidine by different prokaryotic groups in relation to temperature and nutrients in a lacustrine ecosystem. | the incorporation of [3h-methyl] thymidine (3h-tdr) by eubacteria, bacterial groups (alpha- and beta-proteobacteria, cytophaga-flavobacter), and archaea was measured according to temperature (7 and 17 degrees c) and nutrient levels (nitrogen, phosphorus, and carbon) in a lacustrine system (sep, france). short-term incubation was performed using a combination of microautoradiography and fluorescent in situ hybridization. irrespective of the temperatures and nutrients studied, all the major phylog ... | 2006 | 16770684 |
| long term effect of methylparathion contamination on soil microbial community diversity estimated by 16s rrna gene cloning. | the long-term effects of methylparathion contamination on the diversity of soil microbial community was investigated by a culture-independent approach using small subunit ribosomal rna (ssu rrna) gene-based cloning. microbial dna extracted from both the control soil sample and methylparathion contaminated soil sample was subjected to pcr amplification with primers specific for bacterial 16s rrna gene sequences. from the pcr amplification product, clone libraries were constructed for both samples ... | 2006 | 16816989 |
| site-specific variation in antarctic marine biofilms established on artificial surfaces. | the community structure and composition of marine microbial biofilms established on glass surfaces was investigated across three differentially contaminated antarctic sites within mcmurdo sound. diverse microbial communities were revealed at all sites using fluorescence in situ hybridization (fish) and denaturing gradient gel electrophoresis (dgge) techniques. sequencing of excised dgge bands demonstrated close affiliation with known psychrophiles or undescribed bacteria also recovered from the ... | 2006 | 16817926 |
| bacterial diversity of a cyanobacterial mat degrading petroleum compounds at elevated salinities and temperatures. | cyanobacterial mats of the arabian gulf coast of saudi arabia experience extreme conditions of temperature and salinity. because they are exposed to continuous oil pollution, they form ideal models for biodegradation under extreme conditions. we investigated the bacterial diversity of these mats using denaturing gradient gel electrophoresis and 16s rrna cloning, and tested their potential to degrade petroleum compounds at various salinities (fresh water to 16%) and temperatures (5 to 50 degrees ... | 2006 | 16867146 |
| prey selectivity of bacterivorous protists in different size fractions of reservoir water amended with nutrients. | an experiment designed to examine food preferences of heterotrophic nanoflagellates (hnf) grazing on bacterioplankton was performed in the freshwater rímov reservoir (czech republic). water samples were size-fractionated to obtain < 5 microm filtrate containing bacteria and hnf. to manipulate resource availability, < 5 microm treatments were incubated in dialysis bags submerged in the barrels filled with the unfiltered reservoir water amended with either orthophosphate or glucose or combination ... | 2006 | 16872397 |
| peptidoglycan from bacillus cereus mediates commensalism with rhizosphere bacteria from the cytophaga-flavobacterium group. | previous research in our laboratory revealed that the introduction of bacillus cereus uw85 can increase the populations of bacteria from the cytophaga-flavobacterium (cf) group of the bacteroidetes phylum in the soybean rhizosphere, suggesting that these rhizosphere microorganisms have a beneficial relationship (g. s. gilbert, j. l. parke, m. k. clayton, and j. handelsman, ecology 74:840-854, 1993). in the present study, we determined the frequency at which cf bacteria coisolated with b. cereus ... | 2006 | 16885294 |
| niastella koreensis gen. nov., sp. nov. and niastella yeongjuensis sp. nov., novel members of the phylum bacteroidetes, isolated from soil cultivated with korean ginseng. | two novel strains, gr20-10(t) and gr20-13(t), were isolated from soil using r2a medium. the soil sample was collected from a field in the yeongju region of korea that was cultivated with korean ginseng. phylogenetic analysis based on 16s rrna gene sequences indicated that these strains formed a cluster with several uncultured bacterial clones and with flexibacter filiformis, flexibacter sancti, flexibacter japonensis, cytophaga arvensicola and flavobacterium ferrugineum (recently reclassified as ... | 2006 | 16902007 |