Publications

phylogenetic analysis of the human gut microbiota using 16s rdna clone libraries and strictly anaerobic culture-based methods.	the human gut microbiota from three healthy subjects were compared by the use of a sequence analysis of 16s rdna libraries and a culture-based method. direct counts ranged from 1.9 x 10" to 4.0 x 10" cells/g (wet weight), and plate counts totaled 6.6 x 10(10) to 1.2 x 10(11) cfu/g (wet weight). sixty to seventy percent of the bacteria in the human intestinal tract cannot be cultured with currently available methods. the 16s rdna libraries from three subjects were generated from total community d ...	2002	12363017
extra- and intra-cellular lytic effects of cytophaga sp. lr2 on the red microalgae rhodella reticulata.	to evaluate the lytic activities of crude enzymes from cytophaga sp. lr2 on rhodella reticulata cells and isolated algal polysaccharide.	2002	12392519
thermostable aldehyde dehydrogenase from psychrophile, cytophaga sp. kuc-1: enzymological characteristics and functional properties.	we found the occurrence of nad(p)(+)-dependent aldehyde dehydrogenase (ec1.2.1.5) in the cells of a psychrophile from antarctic seawater, cytophaga sp. kuc-1, and purified to homogeneity. about 50% of the enzyme activity remained even after heating at 50 degrees c for 65min and the highest activity was observed in the range of 55-60 degrees c. the enzyme was thermostable and thermophilic, although it was derived from a psychrophile. the circular dichroism at 222nm of the enzyme showed a peak at ...	2002	12419301
analysis of 16s libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria.	total genomic dna from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for pcr amplification of 16s rrna gene sequences with conserved bacterial primers. phylogenetic analysis of the amplification products revealed 40 unique 16s rdna sequences. of these sequences, 25% (10/40) corresponded to described intestinal organisms of the mouse, including lactobacillus spp., helicobacter spp., segmented filamentous bacteria and members of the altered schaed ...	2002	12427955
pharacine, a natural p-cyclophane and other indole derivatives from cytophaga sp. strain am13.1.	from the ethyl acetate extract of the bacterial strain cytophaga sp. am13.1, among many known compounds, the new natural products 2,5-bis(3-indolylmethyl)pyrazine (2) and a highly symmetrical p-cyclophane named pharacine (5) were identified. in addition, tryptamine isovalerate (1) and p-hydroxyphenylacetamide (4), known as plant metabolites, were isolated and characterized from a microorganism for the first time. the new natural products showed no activity against three microalgae, the fungus mu ...	2002	12444694
competitive pcr for quantitation of a cytophaga-flexibacter-bacteroides phylum bacterium associated with the tuber borchii vittad. mycelium.	an uncultured bacterium associated with the ectomycorrhizal fungus tuber borchii vittad. was identified as a novel member of the cytophaga-flexibacter-bacteroides group. utilizing a quantitative pcr targeting the 16s rrna gene, we relatively quantified this bacterium in the host. the estimated number of bacteria was found to be approximately 10(6) cells per 30-day-old t. borchii mycelium culture. this represents the first molecular attempt to enumerate an uncultured bacterium associated with a m ...	2002	12450871
impact of biocontrol strain pseudomonas fluorescens cha0 on rhizosphere bacteria isolated from barley (hordeum vulgare l.) with special reference to cytophaga-like bacteria.	to assess the impact of the biocontrol strain pseudomonas fluorescens cha0 on a collection of barley rhizosphere bacteria using an agar plate inhibition assay and a plant microcosm, focusing on a cha0-sensitive member of the cytophaga-like bacteria (clb).	2002	12452964
automated image analysis and in situ hybridization as tools to study bacterial populations in food resources, gut and cast of lumbricus terrestris l.	an image analysis procedure was developed for bacterial cells after staining with the dna-intercalating dye 4'-6-diamidino-2-phenylindole (dapi), and after in situ hybridization with cy3-labeled, rrna-targeted oligonucleotide probes. dapi- and cy3-images were captured separately from the same scenery with a cooled digital video camera with three ccd chips for the basic colors red (r), green (g) and blue (b). using the appropriate filter sets, images of dapi-stained cells were captured with the r ...	2002	11733082
phylogenetic composition of bacterioplankton assemblages from the arctic ocean.	we analyzed the phylogenetic composition of bacterioplankton assemblages in 11 arctic ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16s rrna genes. the sequencing effort was directed by denaturing gradient gel electrophoresis (dgge) screening of samples and the clone libraries. sequences of 88 clones fell into seven major lineages of the domain bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-p ...	2002	11823184
on the stability properties of a stochastic model for phage-bacteria interaction in open marine environment.	in this paper we extend the deterministic model for the epidemics induced by virulent phages on bacteria in marine environment introduced by beretta and kuang [math. biosci. 149 (1998) 57], allowing random fluctuations around the positive equilibrium. the stochastic stability properties of the model are investigated both analytically and numerically suggesting that the deterministic model is robust with respect to stochastic perturbations.	2002	11825593
anaerophaga thermohalophila gen. nov., sp. nov., a moderately thermohalophilic, strictly anaerobic fermentative bacterium.	the strictly anaerobic gram-negative bacterium strain fru22t grows at 50 degrees c in media containing up to 75 g nacl l(-1). hexoses and pentoses are fermented to equal molar amounts of acetate, propionate and succinate, and no co2 is formed. an orange-red pigment similar to flexirrubin is produced during stationary phase upon exposure to light for several days. cells also produce a surface-active extracellular compound which lowers the surface tension of the medium. this tenside is heat-tolera ...	2002	11837300
diverse bacteria related to the bacteroides subgroup of the cfb phylum within the gut symbiotic communities of various termites.	phylogenetically diverse clones of the partial 16s rdna (ca. 850 bp) of bacteria belonging to the bacteroides subgroup of the cytophaga-flavobacter-bacteroides phylum were collected from the symbiotic microbial communities in the guts of six termite species without cultivation. combined with the sequences reported previously, a total of thirty phylotypes of the subgroup were identified and classified into five phylogenetic clusters. one that was comprised of the phylotypes from a single termite ...	2002	11866123
mutations in flavobacterium johnsoniae gldf and gldg disrupt gliding motility and interfere with membrane localization of glda.	flavobacterium johnsoniae moves rapidly over surfaces by a process known as gliding motility. the mechanism of this form of motility is not known. four genes that are required for f. johnsoniae gliding motility, glda, gldb, gldd, and ftsx, have recently been described. glda is similar to the atp-hydrolyzing components of atp binding cassette (abc) transporters. tn4351 mutagenesis was used to identify two additional genes, gldf and gldg, that are required for cell movement. gldf and gldg appear t ...	2002	11948149
partitioning of bacterial communities between seawater and healthy, black band diseased, and dead coral surfaces.	distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (bbd) on the southern caribbean island of curaçao, netherlands antilles. pcr amplification and sequencing of bacterial 16s rrna genes (rdna) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. the molecular sequences exhibite ...	2002	11976091
response of endophytic bacterial communities in potato plants to infection with erwinia carotovora subsp. atroseptica.	the term endophyte refers to interior colonization of plants by microorganisms that do not have pathogenic effects on their hosts, and various endophytes have been found to play important roles in plant vitality. in this study, cultivation-independent terminal restriction fragment length polymorphism analysis of 16s ribosomal dna directly amplified from plant tissue dna was used in combination with molecular characterization of isolates to examine the influence of plant stress, achieved by infec ...	2002	11976096
spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenerative life support.	bioregenerative life support systems may be necessary for long-term space missions due to the high cost of lifting supplies and equipment into orbit. in this study, we investigated two biological wastewater treatment reactors designed to recover potable water for a spacefaring crew being tested at johnson space center. the experiment (lunar-mars life support test project-phase iii) consisted of four crew members confined in a test chamber for 91 days. in order to recycle all water during the exp ...	2002	11976099
enrichment versus biofilm culture: a functional and phylogenetic comparison of polycyclic aromatic hydrocarbon-degrading microbial communities.	the effect that culture methods have on the diversity of degradative microbial communities is not well understood. we compared conventional batch enrichment with a biofilm culture method for the isolation of polycyclic aromatic hydrocarbon (pah)-degrading microbial communities from a pah-contaminated soil. the two methods were assessed by comparing: (i) the diversity of culturable bacteria; (ii) the diversity of pah-catabolic genes in isolated bacteria; (iii) the inter- and intraspecific diversi ...	2002	12000317
wide bacterial diversity associated with tubes of the vent worm riftia pachyptila.	we carried out a 16s rdna-based molecular survey of the prokaryotic diversity associated with the chitin tubes of the giant vent tubeworm riftia pachyptila (collected at the east pacific rise, 9 degrees n and 13 degrees n). scanning electron microscopy showed dense microbial populations, particularly on the external surface of the middle and upper tube regions, which included very diverse prokaryotic morphotypes. we used archaeal- and bacterial-specific primers for polymerase chain reaction (pcr ...	2002	12010127
a mitochondrial-like aconitase in the bacterium bacteroides fragilis: implications for the evolution of the mitochondrial krebs cycle.	aconitase and isocitrate dehydrogenase (idh) enzyme activities were detected in anaerobically prepared cell extracts of the obligate anaerobe bacteroides fragilis. the aconitase gene was located upstream of the genes encoding the other two components of the oxidative branch of the krebs cycle, idh and citrate synthase. mutational analysis indicates that these genes are cotranscribed. a nonpolar in-frame deletion of the acna gene that encodes the aconitase prevented growth in glucose minimal medi ...	2002	11880608
microbial diversity of a heavily polluted microbial mat and its community changes following degradation of petroleum compounds.	we studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (wadi gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. phormidium- and oscillatoria-like cyanobacterial morphotypes were dominant in the field. bacteria belonging to different groups, mainly the cytophaga-flavobacterium-bacteriodes group, the gamma and beta subclasses of the class p ...	2002	11916684
microheterogeneity in 16s ribosomal dna-defined bacterial populations from a stratified planktonic environment is related to temporal changes and to ecological adaptations.	temporal changes of the bacterioplankton from a meromictic lake (lake vilar, banyoles, spain) were analyzed with four culture-independent techniques: epifluorescence microscopy, pcr-denaturing gradient gel electrophoresis (dgge) fingerprinting, fluorescence in situ whole-cell hybridization and flow cytometry sorting. microscopically, blooms of one cyanobacterium (synechococcus sp.-like), one green sulfur bacterium (chlorobium phaeobacteroides-like), and one purple sulfur bacterium (thiocystis mi ...	2002	11916688
obligate bacterial endosymbionts of acanthamoeba spp. related to the beta-proteobacteria: proposal of 'candidatus procabacter acanthamoebae' gen. nov., sp. nov.	all obligate bacterial endosymbionts of free-living amoebae currently described are affiliated with the alpha-proteobacteria, the chlamydiales or the phylum cytophaga-flavobacterium-bacteroides. here, six rod-shaped gram-negative obligate bacterial endosymbionts of clinical and environmental isolates of acanthamoeba spp. from the usa and malaysia are reported. comparative 16s rdna sequence analysis demonstrated that these endosymbionts form a novel, monophyletic lineage within the beta-proteobac ...	2002	11931173
new degenerate cytophaga-flexibacter-bacteroides-specific 16s ribosomal dna-targeted oligonucleotide probes reveal high bacterial diversity in river taff epilithon.	river microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. in this study the bacterial diversity of river taff epilithon in south wales was investigated. a 16s ribosomal dna (rdna) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. the epilithon was found to be very diverse, with an estimated 59.6% of the bacteri ...	2002	11772628
phylogeny of culturable estuarine bacteria catabolizing riverine organic matter in the northern baltic sea.	the objective of our study was to isolate and determine the phylogenetic affiliation of culturable estuarine bacteria capable of catabolizing riverine dissolved organic matter (rdom) under laboratory conditions. additions of rdom consistently promoted the growth of estuarine bacteria in carbon-limited dilution cultures, with seasonal variation in growth rates and yields. at least 42 different taxa were culturable on solid agar media and, according to quantitative dna-dna hybridizations, constitu ...	2002	11772648
microbial community of a saline mud volcano at san biagio-belpasso, mt. etna (italy).	in san biagio of belpasso, approximately 20 km south of mt. etna, in the area of contact between volcanic and sedimentary formations, a number of small (3- 60 cm in diameter) active mud eruptions discharge co2-rich gases, mud and nacl brines. they can be described as mini-volcanoes owing to their typical conic shapes and continuously bubbling peak craters. samples were collected from the active peak craters at a depth of 20 cm and dna was immediately extracted and amplified with universal 16s rr ...	2002	12030850
cultivation-independent population analysis of bacterial endophytes in three potato varieties based on eubacterial and actinomycetes-specific pcr of 16s rrna genes.	abstract endophytic bacteria are ubiquitous in most plants and colonise plants without exhibiting pathogenicity. studies on the diversity of bacterial endophytes have been mainly approached by characterisation of isolates obtained from internal tissues. despite the broad application of culture-independent techniques for the analysis of microbial communities in a wide range of natural habitats, little information is available on the species diversity of endophytes. in this study, microbial commun ...	2002	19709181
the ecology of cytophaga-flavobacteria in aquatic environments.		2002	19709188
bacterial community composition in the rhizosphere of a transgenic, herbicide-resistant maize (zea mays) and comparison to its non-transgenic cultivar bosphore.	bacterial communities in rhizospheres of transgenic maize (zea mays, with the pat-gene conferring resistance to the herbicide glufosinate; syn. l-phosphinothricin) were compared to its isogenic, non-transgenic cultivar. total dna was extracted from bacterial cell consortia collected from rhizospheres of plants grown in an agricultural field. with the use of three different primer pairs binding to evolutionarily conserved regions of the bacterial 16s rrna gene, partial sequences were amplified by ...	2002	19709208
molecular characterization of microbial community in nitrate-removing activated sludge.	abstract the microbial community composition and dominant denitrifying populations in high-nitrate-removing (cr-i) and low-nitrate-removing (cr-ii) activated sludge from continuous bioreactors were investigated with most probable number (mpn) enumeration, fluorescence in situ hybridization (fish) and 16s rdna characterization. mpns of nitrate-reducing bacteria of sludge cr-i and sludge cr-ii were 2.82x10(7) and 2.69x10(4) colony-forming units ml(-1), respectively. eight denitrifying bacteria and ...	2002	19709242
genetic diversity of 'satellite' bacteria present in cultures of marine diatoms.	abstract uni-algal, non-axenic cultures of six marine diatoms were screened by polymerase chain reaction-denaturing gradient gel electrophoresis for the diversity of the accompanying bacterial communities ('satellite' bacteria) in order to test the hypothesis that algal cells constitute niches for specific bacterial species. the complexity of the satellite assemblages, as judged from the number of detected phylotypes, was low when compared to the complexity of bacterial assemblages in nature. ge ...	2002	19709263
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
analysis of endophytic bacterial communities of potato by plating and denaturing gradient gel electrophoresis (dgge) of 16s rdna based pcr fragments.	the diversity of endophytic bacterial populations of potato (solanum tuberosum cv desirée) was assessed using a combination of dilution plating of plant macerates followed by isolation and characterization of isolates, and direct pcr-dgge on the basis of dna extracted from plants. the culturable endophytic bacterial communities detected in potato stem bases as well as in roots were in most cases on the order 103 to 105 cfu g?1 of fresh plant tissue. dilution plating revealed that a range of bact ...	2001	12032611
[isolation and characterization of cytophaga lytica lipopolysaccharide].	lipopolysaccharide (lps) and its structural components: lipid a, o-specific polysaccharide (o-ps) and oligosaccharide core (og-core) have been isolated from cytophaga lytica. 3-oxytetradecanoic (40.8%) and dodecanoic (28.7%) are the predominant fatty acids of lipid a; pentadecanoic (6.8%), 3-oxyhexadecanoic (6.5%) as well as hexadecanoic (5.4%) acids have been found as well. the content of the rest of fatty acids is inconsiderable (2.3 to 0.5%). og-core contained monosaccharides both typical of ...	2001	11785415
community dynamics of free-living and particle-associated bacterial assemblages during a freshwater phytoplankton bloom.	bacterial community dynamics were followed in a 19-day period during an induced diatom bloom in two freshwater mesocosms. the main goal was to compare diversity and succession among free-living (<10 mm) and particle-associated (>10 mm) bacteria. denaturing gradient gel electrophoresis (dgge) of pcr amplified 16s rdna showed the highest number of bands among free-living bacteria, but with a significant phylogenetic overlap in the two size fractions indicating that free-living bacteria were also i ...	2001	12024253
changes in the epilimnetic bacterial community composition, production, and protist-induced mortality along the longitudinal axis of a highly eutrophic reservoir.	we studied changes in the epilimnetic bacterial community composition (bcc), bacterial biomass and production, and protistan succession and bacterivory along the longitudinal axis of the canyon-shaped, highly eutrophic sau reservoir (ne spain) during two sampling campaigns, in april and july 1997. longitudinal changes in bcc from the river inflow to the dam area of the reservoir were detected by using oligonucleotide probes targeted to the kingdom bacteria, to the alpha, beta, and gamma subclass ...	2001	12024261
phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (brassica napus cv. westar) employing cultivation-dependent and cultivation-independent approaches.	the structure of the microbial rhizoplane community of the important crop plant oilseed rape was studied by using a culture-dependent as well as a culture-independent approach based on 16s rdna amplification. after isolation of the microbial community from the rhizoplane of oilseed rape (brassica napus cv. westar), the collected suspension was divided into two parts. one part was used for cultivation of bacteria onto three different growth media to establish a culture collection. from the other ...	2001	12024277
viable cytophaga-like bacterium in the 0.2 microm-filtrate seawater.	a strain of the cytophaga-like bacterium (clb), nano-1, was isolated from the 0.2 microm-filtrate of natural seawater. both cellular fatty acid and 16s rdna sequence analyses indicated that nano-1 is closely affiliated to the marine gliding clb genus, microscilla. nano-1 was observed to undergo cyclic morphological change typical of the genus microscilla, and sub-0.2-microm cells were formed in the late stationary phase. the sub-0.2-microm cells were repeatedly revived and subcultured. formation ...	2001	11876369
muricauda ruestringensis gen. nov., sp. nov., a facultatively anaerobic, appendaged bacterium from german north sea intertidal sediment.	a gram-negative, facultatively anaerobic bacterium with appendages was isolated from continuous cultures with a seawater-sediment suspension containing hexadecane as the sole carbon source. although this organism was isolated from a hexadecane-degrading bacterial community, it was not able to degrade hexadecane. however, this bacterium was able to use different sugars and amino acids for growth, indicating that it probably profits from the lysis or from products like surfactants of other cells i ...	2001	11760940
bacterial gliding motility: multiple mechanisms for cell movement over surfaces.	the mechanisms responsible for bacterial gliding motility have been a mystery for almost 200 years. gliding bacteria move actively over surfaces by a process that does not involve flagella. gliding bacteria are phylogenetically diverse and are abundant in many environments. recent results indicate that more than one mechanism is needed to explain all forms of bacterial gliding motility. myxococcus xanthus "social gliding motility" and synechocystis gliding are similar to bacterial "twitching mot ...	2001	11544349
comparative genomics and evolution of genes encoding bacterial (p)ppgpp synthetases/hydrolases (the rel, rela and spot proteins).	in the gram-negative model organism escherichia coli, the effector molecule of the stringent response, (p)ppgpp, is synthesized by two different enzymes, rela and spot, whereas in the gram-positive model organism bacillus subtilis only one enzyme named rel is responsible for this activity. rel and spot also possess (p)ppgpp hydrolase activity. blast searches were used to identify orthologous genes in databases. the construction and bootstrapping of phylogenetic trees allowed classification of th ...	2001	11545276
polyamine distribution profiles in newly validated genera and species within the flavobacterium-flexibacter-cytophaga-sphingobacterium complex.	cellular polyamines of 58 strains belonging to the flavobacterium-flexibacter-cytophaga-sphingobacterium complex were analysed by hplc. homospermidine was found in all species of flavobacterium, chryseobacterium, empedobacter, myroides, cellulophaga, salegentibacter, psychroserpens and gelidibacter of the family flavobacteriaceae. flavobacterium ferrugineum located outside of this family also contained homospermidine. cytophaga fermentans and c. xylanolytica belonging to the family bacteroidacea ...	2001	11548199
members of the cytophaga-flavobacterium-bacteroides phylum as intracellular bacteria of acanthamoebae: proposal of 'candidatus amoebophilus asiaticus'.	three gram-negative, rod-shaped bacteria that were found intracellularly in two environmental and one clinical acanthamoeba sp. isolates were analysed. two endocytobionts showing a parasitic behaviour were propagated successfully outside their amoebal host cells and were identified subsequently by comparative 16s rrna sequence analysis as being most closely affiliated with flavobacterium succinicans (99% 16s rrna sequence similarity) or flavobacterium johnsoniae (98% 16s rrna sequence similarity ...	2001	11553234
adhesion of the fish pathogen flavobacterium psychrophilum to unfertilized eggs of rainbow trout (oncorhynchus mykiss) and n-hexadecane.	the ability of flavobacterium psychrophilum, the causative agent of rainbow trout fry syndrome (rtfs) in fish, to attach to unfertilized rainbow trout (oncorhynchus mykiss) eggs and to hydrocarbon n-hexadecane was examined in the present study.	2001	11555199
a newly discovered bacterium associated with parthenogenesis and a change in host selection behavior in parasitoid wasps.	the symbiotic bacterium wolbachia pipientis has been considered unique in its ability to cause multiple reproductive anomalies in its arthropod hosts. here we report that an undescribed bacterium is vertically transmitted and associated with thelytokous parthenogenetic reproduction in encarsia, a genus of parasitoid wasps. although wolbachia was found in only one of seven parthenogenetic encarsia populations examined, the "encarsia bacterium" (eb) was found in the other six. among seven sexually ...	2001	11592990
phylogenetic analysis and taxonomic study of marine cytophaga-like bacteria: proposal for tenacibaculum gen. nov. with tenacibaculum maritimum comb. nov. and tenacibaculum ovolyticum comb. nov., and description of tenacibaculum mesophilum sp. nov. and tenacibaculum amylolyticum sp. nov.	bacterial strains were isolated from sponge and green algae which were collected on the coast of japan and palau. the phylogenetic relationships of these isolates among marine species of the cytophaga-flavobacterium-bacteroides complex were analysed by using their gyrb nucleotide sequences and translated peptide sequences (gyrb) in addition to 16s rdna sequences. these isolates were closely related to the previously characterized marine flexibacter species, [flexibacter] maritimus and [flexibact ...	2001	11594591
effect of sampling method on the representative recovery of microorganisms from the surfaces of aquacultured finfish.	the objective of this study was to determine if a gentle rinse procedure was equivalent to the combination of excision and homogenization with a stomacher for the relative removal of various microorganisms from finfish fillets. fillets of hybrid striped bass and rainbow trout were obtained from local markets and sampled using three methods: rinse (r), excision followed by homogenization in a stomacher (s), and homogenization of fillets following a rinse (rs). microorganisms were enumerated on se ...	2001	11601699
isolation of novel pelagic bacteria from the german bight and their seasonal contributions to surface picoplankton.	we tested new strategies for the isolation of abundant bacteria from coastal north sea surface waters, which included reducing by several orders of magnitude the concentrations of inorganic n and p compounds in a synthetic seawater medium. agar plates were resampled over 37 days, and slowly growing colonies were allowed to develop by repeatedly removing all newly formed colonies. a fivefold increase of colonies was observed on plates with reduced nutrient levels, and the phylogenetic composition ...	2001	11679337
comparison of cellular and biomass specific activities of dominant bacterioplankton groups in stratified waters of the celtic sea.	a flow-sorting technique was developed to determine unperturbed metabolic activities of phylogenetically characterized bacterioplankton groups with incorporation rates of [(35)s]methionine tracer. according to fluorescence in situ hybridization with rrna targeted oligonucleotide probes, a clade of alpha-proteobacteria, related to roseobacter spp., and a cytophaga-flavobacterium cluster dominated the different groups. cytometric characterization revealed both these groups to have high dna (hna) c ...	2001	11679347
isolation of bacteria and 16s rdnas from lake vostok accretion ice.	lake vostok, the largest subglacial lake in antarctica, is separated from the surface by approximately 4 km of glacial ice. it has been isolated from direct surface input for at least 420 000 years, and the possibility of a novel environment and ecosystem therefore exists. lake vostok water has not been sampled, but an ice core has been recovered that extends into the ice accreted below glacial ice by freezing of lake vostok water. here, we report the recovery of bacterial isolates belonging to ...	2001	11683867
biodegradation of methyl tert-butyl ether under various substrate conditions.	five aerobic enrichments efficient at degrading methyl tert-butyl ether (mtbe) under different substrate conditions were developed in well-mixed reactors containing a polyethlene porous pot for biomass retention. the five substrate conditions were as follows: mtbe alone; mtbe and diethyl ether (dee); mtbe and diisopropyl ether (dipe); mtbe and ethanol (etoh); and mtbe with benzene, toluene, ethylbenzene, and xylene (btex). all five cultures demonstrated greater than 99.9% removal of mtbe. additi ...	2001	11718336
quantitative molecular analysis of the microbial community in marine arctic sediments (svalbard).	fluorescence in situ hybridization (fish) and rrna slot blot hybridization with 16s rrna-targeted oligonucleotide probes were used to investigate the phylogenetic composition of a marine arctic sediment (svalbard). fish resulted in the detection of a large fraction of microbes living in the top 5 cm of the sediment. up to 65.4% +/- 7.5% of total dapi (4',6'-diamidino-2-phenylindole) cell counts hybridized to the bacterial probe eub338, and up to 4.9% +/- 1.5% hybridized to the archaeal probe arc ...	2001	11133470
phylogenetic diversity of bacteria associated with the marine sponge rhopaloeides odorabile.	molecular techniques were employed to document the microbial diversity associated with the marine sponge rhopaloeides odorabile. the phylogenetic affiliation of sponge-associated bacteria was assessed by 16s rrna sequencing of cloned dna fragments. fluorescence in situ hybridization (fish) was used to confirm the presence of the predominant groups indicated by 16s rdna analysis. the community structure was extremely diverse with representatives of the actinobacteria, low-g+c gram-positive bacter ...	2001	11133476
microbial community dynamics in mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations.	a mesocosm experiment was performed to study the influence of nutrients on activity and diversity of bacterial assemblages from the mediterranean sea. changes in the diversity of the predominant bacterial populations were monitored by dgge fingerprinting of pcr products derived from 16s rrna encoding genes. fluctuations in the diversity of the most active populations was inferred by performing the dgge fingerprinting on the basis of the cellular rrna after reverse transcription and pcr amplifica ...	2001	11137604
microbial community dynamics in mediterranean nutrient-enriched seawater mesocosms: changes in abundances, activity and composition.	quantitative and qualitative changes in bacterial communities from the mediterranean sea were compared in duplicate batch mesocosms with or without addition of inorganic nutrients. methods including traditional microbial ecology techniques, molecular biology and flow cytometry were combined to determine abundances, production, cell size, activity, culturability and taxonomic diversity of bacterial cells. addition of nutrients and confinement resulted in an increase of bacterial densities which w ...	2001	11137605
alpha- and beta-proteobacteria control the consumption and release of amino acids on lake snow aggregates.	we analyzed the composition of aggregate (lake snow)-associated bacterial communities in lake constance from 1994 until 1996 between a depth of 25 m and the sediment surface at 110 m by fluorescent in situ hybridization with rrna-targeted oligonucleotide probes of various specificity. in addition, we experimentally examined the turnover of dissolved amino acids and carbohydrates together with the microbial colonization of aggregates formed in rolling tanks in the lab. generally, between 40 and m ...	2001	11157226
impact of uv radiation on bacterioplankton community composition.	the potential effect of uv radiation on the composition of coastal marine bacterioplankton communities was investigated. dilution cultures with seawater collected from the surface mixed layer of the coastal north sea were exposed to different ranges of natural or artificial solar radiation for up to two diurnal cycles. the composition of the bacterioplankton community prior to exposure was compared to that after exposure to the different radiation regimes using denaturing gradient gel electropho ...	2001	11157229
phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream.	we used in situ hybridization with fluorescently labeled rrna-targeted oligonucleotide probes concurrently with measurements of bacterial carbon production, biomass, and extracellular polymeric substances (eps) to describe the bacterial community in sediments along a glacial stream. the abundance of sediment-associated archaea, as detected with the arch915 probe, decreased downstream of the glacier snout, and a major storm increased their relative abundance by a factor of 5.5 to 7.9. bacteria of ...	2001	11157246
pcr primers and functional probes for amplification and detection of bacterial genes for extracellular peptidases in single strains and in soil.	a set of primers and functional probes was developed for the detection of peptidase gene fragments of proteolytic bacteria. based on dna sequence data, degenerate pcr primers and internal dig-labeled probes specific for genes encoding alkaline metallopeptidases (apr) (e.3.4.24), neutral metallopeptidases (npr) (e.3.4.24) and serine peptidases (sub) (e.3.4.21) were derived by multiple sequence alignments. type strains with known peptidase genes and proteolytic bacteria from a grassland rhizospher ...	2001	11165346
bacterial populations colonizing and degrading rice straw in anoxic paddy soil.	rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. the bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. rice straw was incubated in paddy soil anaerobically for 71 days. denaturing gradient gel electrophoresis (dgge) of the amplified bacterial 16s rrna genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incub ...	2001	11229927
phylogenetic analysis of the succession of bacterial communities in the great south bay (long island).	bacterial community composition and succession were examined over the course of the summer season in the great south bay, long island, ny, usa, using a 16s rdna clone library approach. there was a progression of changes in dominant species in the libraries during the summer of 1997. the july library had several groups dominant, the sar407 relatives of the alpha-proteobacteria (24%) and the sar86 (18%), sulfur-oxidizing symbiont relatives (8%) of the gamma-proteobacteria, and unidentified cytopha ...	2001	11248393
phylogenetic diversity of bacterial and archaeal communities in the anoxic zone of the cariaco basin.	microbial community samples were collected from the anoxic zone of the cariaco basin at depths of 320, 500, and 1,310 m on a november 1996 cruise and were used to construct 16s ribosomal dna libraries. of 60 nonchimeric sequences in the 320-m library, 56 belonged to the epsilon subdivision of the proteobacteria (epsilon-proteobacteria) and 53 were closely related to ectosymbionts of rimicaris exoculata and alvinella pompejana, which are referred to here as epsilon symbiont relatives (esr). the 5 ...	2001	11282619
16s rdna diversity of cultured and uncultured prokaryotes of a mat sample from lake fryxell, mcmurdo dry valleys, antarctica.	the prokaryotic diversity of aerobic and anaerobic bacterial isolates and of bacterial and archaeal 16s rdna clones was determined for a microbial mat sample from the moated region of lake fryxell, mcmurdo dry valleys, antarctica. among the anaerobic bacteria, members of clostridium estertheticum and some other psychrotolerant strains dominated whereas methanogens and other archaea were lacking. isolates highly related to flavobacterium hibernum, janthiniobacterium lividum, and arthrobacter flav ...	2001	11302499
the microbial diversity in picoplankton enrichment cultures: a molecular screening of marine isolates.	picoplankton bacteria from a north sea water sample were cultured under a variety of different conditions (nutrients, temperature, light, agitation, adhesion). fluorescent in situ hybridization (fish) analysis of the enrichments showed complex communities which were dominated by gamma-proteobacteria or beta-proteobacteria, followed by alpha-proteobacteria and bacteria from the cytophaga/flavobacterium/bacteroides (cfb) cluster. among 410 isolates, a high degree of diversity was found, both with ...	2001	11311435
a molecular phylogenetic survey of sea-ice microbial communities (simco).	16s rdna clone library analysis was used to identify bacterial biodiversity in a variety of sea-ice microbial communities (simco). dna was extracted from seven antarctic sea-ice samples and one arctic sea-ice sample and 16s rdna pcr-amplified using universal and archaea-specific primers. recombinant 16s rdna clones were obtained and dereplicated using restriction fragment length polymorphism analysis (rflp). after rflp analysis, 100 distinct phylotypes (a unique clone or group of clones with seq ...	2001	11311437
2-bromoethanesulfonate affects bacteria in a trichloroethene-dechlorinating culture.	long-term exposure to 2-bromoethanesulfonate (bes), an agent known to inhibit methanogenesis, altered the bacterial community structure of an anaerobic enrichment culture that reductively dechlorinated trichloroethene (tce). bes did not hinder the dechlorination of tce or other chlorinated ethenes as previously reported, although different intermediates and end products were observed.	2001	11319126
in situ identification of polyphosphate- and polyhydroxyalkanoate-accumulating traits for microbial populations in a biological phosphorus removal process.	polyphosphate- and polyhydroxyalkanoate (pha)-accumulating traits of predominant microorganisms in an efficient enhanced biological phosphorus removal (ebpr) process were investigated systematically using a suite of non-culture-dependent methods. results of 16s rdna clone library and fluorescence in situ hybridization (fish) with rrna-targeted, group-specific oligonucleotide probes indicated that the microbial community consisted mostly of the alpha- (9.5% of total cells), beta- (41.3%) and gamm ...	2001	11321541
clogging of a limestone fracture by stimulating groundwater microbes.	biological clogging is promoted in aquifers either to contain or to remediate groundwater. in this study, an apparatus able to detect small changes in hydraulic conductivity (k) was developed to measure the clogging of a single fracture in limestone, following microbial stimulation. the fracture had a 2.5 mm2 section and was 50 cm long. prior to the inoculation of the limestone, the sequencing of representative clones from 16s rrna genes isolated from groundwater, showed significant affiliation ...	2001	11337851
phylogenetic analyses of caulerpa taxifolia (chlorophyta) and of its associated bacterial microflora provide clues to the origin of the mediterranean introduction.	the accidental introduction of caulerpa taxifolia into the mediterranean is no longer under dispute. what has eluded researchers until now, is definitive evidence for the original, biogeographical source population. here we present two independent lines of evidence that support an australian origin for the mediterranean populations of c. taxifolia. first, we reanalysed algal rdna-internal transcribed spacer (rdna-its) sequences, combining previously published sequences from different studies wit ...	2001	11348502
molecular detection of marine bacterial populations on beaches contaminated by the nakhodka tanker oil-spill accident.	in january 1997, the tanker nakhodka sank in the japan sea, and more than 5000 tons of heavy oil leaked. the released oil contaminated more than 500 km of the coastline, and some still remained even by june 1999. to investigate the long-term influence of the nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturi ...	2001	11359510
changes in bacterial community composition and dynamics and viral mortality rates associated with enhanced flagellate grazing in a mesoeutrophic reservoir.	bacterioplankton from a meso-eutrophic dam reservoir was size fractionated to reduce (<0.8-microm treatment) or enhance (<5-microm treatment) protistan grazing and then incubated in situ for 96 h in dialysis bags. time course samples were taken from the bags and the reservoir to estimate bacterial abundance, mean cell volume, production, protistan grazing, viral abundance, and frequency of visibly infected cells. shifts in bacterial community composition (bcc) were examined by denaturing gradien ...	2001	11375187
study of microbial community of brewery-treating granular sludge by denaturing gradient gel electrophoresis of 16s rrna gene.	the microbial community structure of granular sludge from an upflow anaerobic sludge blanket (uasb) reactor treating brewery effluent was studied by denaturing gradient gel electrophoresis (dgge). twelve major bands were observed in the dgge fingerprint for the bacteria domain and four bands for the archaea domain. of the bacterial bands observed, six were successfully purified and sequenced. among them, three were related to the gram-positive low g + c group, one to the delta subclass of the pr ...	2001	11379115
16s rrna in situ probing for the determination of the family level community structure implicated in enhanced biological nutrient removal.	knowledge of a discrete physiological group capable of excess biological phosphate removal (ebpr) remains unclear. consequently, microbial community analysis of an enhanced continuous laboratory-scale activated sludge process displaying a strong ebpr mechanism was conducted. unit design was configured upon the three-stage phoredox process and characterization of the activated sludge bacterial community was carried out using fluorescent in situ hybridization (fish) techniques. fixed activated slu ...	2001	11379117
in situ polychlorophenol bioremediation potential of the indigenous bacterial community of boreal groundwater.	the composition and chlorophenol-degrading potential of groundwater bacterial community in a permanently cold, oxygen-deficient chlorophenol contaminated aquifer at kärkölä, finland was studied with the aim of evaluating in situ bioremediation potential. the groundwater contained from 10(4) to 10(7) microscopically counted cells/ml and up to 10(5) cfu/ml heterotrophic bacteria cultivable at 8 and 20 degrees c. of the 102 pure cultures, of which 86% gram-negative, from the plume area (10,000 micr ...	2001	11394785
characterization of facultative oligotrophic bacteria from polar seas by analysis of their fatty acids and 16s rdna sequences.	one hundred and seventy three bacterial strains, isolated previously after enrichment under oligotrophic, psychrophylic conditions from arctic (98 strains) and antarctic seawater (75 strains), were characterized by gas-liquid chromatographic analysis of their fatty acid compositions. by numerical analysis, 8 clusters, containing 2 to 59 strains, could be delineated, and 8 strains formed separate branches. five clusters contained strains from both poles, two minor clusters were confined to arctic ...	2001	11403404
zobellia galactanovorans gen. nov., sp. nov., a marine species of flavobacteriaceae isolated from a red alga, and classification of [cytophaga] uliginosa (zobell and upham 1944) reichenbach 1989 as zobellia uliginosa gen. nov., comb. nov.	a mesophilic, aerobic, non-flagellated, gliding bacterium, forming yellow colonies and designated dsijt, was isolated from a red alga on the sea-shore of roscoff, brittany, france. dsijt was selected for its ability to actively degrade both agars and carrageenans. the gram-negative cells occurred singly or in pairs as long rods. the temperature range for growth was 13-45 degrees c, with an optimum at 35 degrees c. the ph range for growth at 35 degrees c was from 6.0 to 8.5, with an optimum aroun ...	2001	11411725
microbial populations associated with treatment of an industrial dye effluent in an anaerobic baffled reactor.	fluorescent in situ hybridization (fish) using 16s and 23s rrna-targeted probes together with construction of an archaeal 16s ribosomal dna (rdna) clone library was used to characterize the microbial populations of an anaerobic baffled reactor successfully treating industrial dye waste. wastewater produced during the manufacture of food dyes containing several different azo and other dye compounds was decolorized and degraded under sulfidogenic and methanogenic conditions. use of molecular metho ...	2001	11425746
the contribution of halophilic bacteria to the red coloration of saltern crystallizer ponds(1).	analysis of the pigments extracted from solar saltern crystallizer ponds in santa pola near alicante and on the balearic island of mallorca, spain, showed that 5-7.5% of the total prokaryotic pigment absorbance could be attributed to a novel carotenoid or carotenoid-like compound. this unidentified pigment was identical to the sole pigment present in salinibacter ruber, the only described member of a newly discovered genus of red halophilic bacteria related to the cytophaga-flavobacterium-bacter ...	2001	11451516
multitude and temporal variability of ecological niches as indicated by the diversity of cultivated bacterioplankton.	the diversity of cultured planktonic bacteria was analyzed. bacterial strains were isolated from a eutrophic lake (zwischenahner meer, niedersachsen, germany) at three different sampling dates (october 1997, april and may 1998). phylogenetic diversity was assessed by polymerase chain reaction (pcr), denaturing gradient gel electrophoresis (dgge), and sequencing of 16s rrna gene fragments. enterobacterial repetitive intergenic consensus (eric)-pcr revealed a high genomic diversity within the stra ...	2001	11451519
growth of chitinolytic dune soil beta-subclass proteobacteria in response to invading fungal hyphae.	it has frequently been reported that chitinolytic soil bacteria, in particular biocontrol strains, can lyse living fungal hyphae, thereby releasing potential growth substrate. however, the conditions used in such assays (high bacterial density, rich media, fragmented hyphae) make it difficult to determine whether mycolytic activity is actually of importance for the growth and survival of chitinolytic bacteria in soils. an unidentified group of beta-subclass proteobacteria (cbetaps) was most domi ...	2001	11472904
flavobacterium frigidarium sp. nov., an aerobic, psychrophilic, xylanolytic and laminarinolytic bacterium from antarctica.	a psychrophilic, aerobic bacterium designated a2it was isolated from marine sediment recovered from shallow waters surrounding adelaide island, antarctica (67 degrees 34' s, 68 degrees 07' w). the organism exhibited xylanolytic and laminarinolytic activity and was halotolerant. basic characterization showed that it was gram-negative, non-motile, yellow-pigmented (beta,beta-carotene-3,3'-diol) and positive for oxidase and catalase synthesis. analysis of the 16s rdna sequence suggests that the org ...	2001	11491319
polyamine distribution profiles in the eighteen genera phylogenetically located within the flavobacterium-flexibacter-cytophaga complex.	cellular polyamines of eighteen genera belonging to the flavobacterium-flexibacter-cytophaga complex were analysed by ion exchange liquid chromatography. homospermidine was the major polyamine in the genera bergeyella, riemerella, ornithobacterium, weeksella, capnocytophaga, polaribacter and psychroflexus belonging to the family flavobacteriaceae. in the family spirosomaceae, runella, spirosoma and flectobacillus species contained spermidine whereas cyclobacterium species contained homospermidin ...	2001	11491527
systematics and evolution of ruminal species of the genus prevotella.	bacterial species of the genus prevotella represent a numerically dominant microbial population in the rumen of cattle. they belong to the phylogenetic division cytophaga-flexibacter-bacteroides (cfb) which is a large group of ecologically diverse bacteria with only a few shared traits. the phylogenetic descent from a common ancestor seems to be unquestionable, however, as judged from the small subunit ribosomal rna analysis. only 4 ruminal prevotella species have been described to date, even th ...	2001	11501474
psychrophilic valine dehydrogenase of the antarctic psychrophile, cytophaga sp. kuc-1: purification, molecular characterization and expression.	we found the occurrence of valine dehydrogenase in the cell extract of a psychrophilic bacterium, cytophaga sp. kuc-1, isolated from antarctic seawater and purified the enzyme to homogeneity. the molecular mass of the enzyme was determined to be approximately 154 kda by gel filtration and that of the subunit was 43 kda by sds/page: the enzyme was a homotetramer. the enzyme required nad+ as a coenzyme, and catalyzed the oxidative deamination of l-valine, l-isoleucine, l-leucine and the reductive ...	2001	11502197
molecular identification of microorganisms from endodontic infections.	a relatively wide range of bacteria have been isolated from root canals using standard culture techniques. however, only 50% of the bacteria in the oral cavity are cultivable (s. s. socransky et al., arch. oral biol. 8:278-280, 1963); hence, bacterial diversity in endodontic infections is underestimated. this study used a pcr-based 16s rrna gene assay, followed by cloning and sequencing of 16s rrna amplicons from a small subset of samples to assess the diversity of bacteria present in infected r ...	2001	11526164
the use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that fibrobacter diverged at a similar time to chlamydia and the cytophaga-flavobacterium-bacteroides division.	the phylogenetic placement of the rumen bacterium fibrobacter succinogenes was determined using a signature sequence approach that allows determination of the relative branching order of the major divisions among bacteria [gupta, r. s. (2000) fems microbiol rev 24, 367-402]. for this purpose, segments of the hsp60 (groel), hsp70 (dnak), ctp synthase and alanyl-trna synthetase genes, which are known to contain signature sequences that are useful for phylogenetic deterministic purposes, were clone ...	2001	11535801
the branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins.	the presence of shared conserved inserts and deletions (indels or signature sequences) in proteins provides a powerful means for understanding the evolutionary relationships among the bacteria. using such indels, all of the main groups within the bacteria can be defined in clear molecular terms and it has become possible to deduce that they branched from a common ancestor in the following order: low g + c gram-positive --> high g+c gram-positive --> deinococcus thermus --> cyanobacteria --> spir ...	2001	12051562
[properties and mechanisms of marine polysaccharidases].		2001	12552838
[clusterization of halophilic and halotolerant eubacteria using whole-cell protein electrophoresis data].	total cell proteins of the nineteen halophilic and halotolerant eubacteria isolated from marine sediments and highly mineralized formation waters of oil fields were investigated by sds gel electrophoresis. the microorganisms studied, phenotypically identified as belonging to the genera dietzia, rhodococcus, staphylococcus, cytophaga, brevibacterium, and archangium, were found to form clearly distinguishable clusters (20-30% similarity at the generic level) on the dendrogram derived from electrop ...	2000	11315673
investigation of 0.2 µm filterable bacteria from the western mediterranean sea using a molecular approach: dominance of potential starvation forms.	although the existence of 0.2 µm filterable bacteria has been known since the early 80's, they are not taken into consideration when modeling microbial food webs, due to an overall lack of information concerning this specific size class. according to physiological studies on starvation forms and investigations on small bacterial cells in marine ecosystems, a 0.2 µm filtrate may consist of different phenotypes: starvation forms of typical marine bacteria, ultramicrobacteria or bacterial cells, ev ...	2000	10640668
cloning and characterization of the flavobacterium johnsoniae gliding-motility genes gldb and gldc.	the mechanism of bacterial gliding motility (active movement over surfaces without the aid of flagella) is not known. a large number of mutants of the gliding bacterium flavobacterium johnsoniae (cytophaga johnsonae) with defects in gliding motility have been previously isolated, and genetic techniques to analyze these mutants have recently been developed. we complemented a nongliding mutant of f. johnsoniae (uw102-99) with a library of wild-type dna by using the shuttle cosmid pcp26. the comple ...	2000	10648514
identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis.	the microbial assemblages of lake cisó and lake vilar (banyoles, northeast spain) were analyzed in space and time by microscopy and by performing pcr-denaturing gradient gel electrophoresis (dgge) and sequence analysis of 16s rrna gene fragments. samples obtained from different water depths and at two different times of the year (in the winter during holomixis and in the early spring during a phytoplankton bloom) were analyzed. although the lakes have the same climatic conditions and the same wa ...	2000	10653710
increase in bacterial community diversity in subsurface aquifers receiving livestock wastewater input.	despite intensive studies of microbial-community diversity, the questions of which kinds of microbial populations are associated with changes in community diversity have not yet been fully solved by molecular approaches. in this study, to investigate the impact of livestock wastewater on changes in the bacterial communities in groundwater, bacterial communities in subsurface aquifers were analyzed by characterizing their 16s rdna sequences. the similarity coefficients of restriction fragment len ...	2000	10698758
selected chitinase genes in cultured and uncultured marine bacteria in the alpha- and gamma-subclasses of the proteobacteria.	pcr primers were patterned after chitinase genes in four gamma-proteobacteria in the families alteromonadaceae and enterobacteriaceae (group i chitinases) and used to explore the occurrence and diversity of these chitinase genes in cultured and uncultured marine bacteria. the pcr results from 104 bacterial strains indicated that this type of chitinase gene occurs in two major groups of marine bacteria, alpha- and gamma-proteobacteria, but not the cytophaga-flavobacter group. group i chitinase ge ...	2000	10698791
changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques.	dilution cultures are a common technique for measuring the growth of bacterioplankton communities. in this study, the taxonomic composition of marine bacterioplankton dilution cultures was followed in water samples from plymouth sound and the english channel (uk). bacterial abundances as well as protein and dna content were closely monitored by flow cytometry. denaturing gradient gel electrophoresis (dgge) of polymerase chain reaction (pcr)-amplified 16s rdna fragments and fluorescence in situ h ...	2000	11220305
news & notes: detection of microorganisms with overall cellulolytic activity.	a modification is described of the plate method for the detection of microorganisms with overall cellulolytic activity, including those like cytophaga, in which the activity is cell bound. within a few days of incubation colonies of cellulose-degrading bacteria formed holes in discs of lens paper placed on freshly inoculated agar plates.	2000	10594230
influence of physiological factors on the lysis effect of cytophaga on the red microalga rhodella reticulata.	the influence of different factors on the lysis of the red microalga, rhodella reticulata, by cytophaga sp. lr2 was studied. the pathogenic bacterial strain was more resistant than the alga to the physiological parameters studied, which assured long-term survival of bacteria in algal cultures. cytophaga sp. lr2 infected r. reticulata at temperatures between 15 and 30 degrees c, in the illuminated as well as the non-illuminated cultures, at ph values between 5.0 and 9.0, and in the presence of na ...	2000	10736006
use of length heterogeneity pcr and fatty acid methyl ester profiles to characterize microbial communities in soil.	in length heterogeneity pcr (lh-pcr) a fluorescently labeled primer is used to determine the relative amounts of amplified sequences originating from different microorganisms. labeled fragments are separated by gel electrophoresis and detected by laser-induced fluorescence with an automated gene sequencer. we used lh-pcr to evaluate the composition of the soil microbial community. four soils, which differed in terms of soil type and/or crop management practice, were studied. previous data for mi ...	2000	10742258
natural assemblages of marine proteobacteria and members of the cytophaga-flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter.	we used a method that combines microautoradiography with hybridization of fluorescent rrna-targeted oligonucleotide probes to whole cells (micro-fish) to test the hypothesis that the relative contributions of various phylogenetic groups to the utilization of dissolved organic matter (dom) depend solely on their relative abundance in the bacterial community. we found that utilization of even simple low-molecular-weight dom components by bacteria differed across the major phylogenetic groups and o ...	2000	10742262
phylogenetic characterization of a novel radiation-resistant bacterium from irradiated pork: description of hymenobacter actinosclerus sp. nov.	a phylogenetic analysis was performed on a red-pigmented, radiation-resistant, gram-negative, rod-shaped organism originating from irradiated pork. comparative 16s rrna gene sequencing showed the bacterium was a member of the cytophaga-flavobacterium-bacteroides line of descent and represents a new subline within the genus hymenobacter. a new species, hymenobacter actinosclerus, is described for this novel radiation-resistant bacterium. the type strain of hymenobacter actinosclerus is ccug 39621 ...	2000	10758882