| 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 |
| evolutionary relationships among photosynthetic bacteria. | to understand the evolution of photosynthetic bacteria it is necessary to understand how the main groups within bacteria have evolved from a common ancestor, a critical issue that has not been resolved in the past. recent analysis of shared conserved inserts or deletions (indels) in protein sequences has provided a powerful means to resolve this long-standing problem in microbiology. based on a set of 25 indels in highly conserved and widely distributed proteins, all main groups within bacteria ... | 2003 | 16228576 |
| 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 |
| 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 |
| 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 |
| bacteria associated with the surface and gut of marine copepods. | little is known about the nature of bacteria associated with the surface and gut of marine copepods, either in laboratory-reared animals or in the natural environment. nor is it known whether such animals possess a gut flora. the present report deals with studies of microorganisms isolated from healthy, laboratory-reared copepods of the species acartia tonsa dana, from several species of wild copepods collected from a marine or estuarine environment, and from laboratory dishes containing moribun ... | 1979 | 16345368 |
| occurrence of cytophagas in sewage plants. | with the application of plate count methods and of the koh-flexirubin test, bacteria belonging to the cytophaga group were proved to occur regularly in samples from biological sewage treatment facilities. generally, the percentage of cytophaga colonies of the total heterotrophic colonies was lowest in the inflow sewage water as compared with the values found in activated sludge, trickling filter, and effluent samples. during an observation period of 16 months, the highest percentages of cytophag ... | 1980 | 16345539 |
| influence of temperature adaptation on glucose metabolism in a psychrotrophic strain of cytophaga johnsonae. | selective enrichment of yellow-orange-pigmented, gram-negative bacteria related to cytophaga johnsonae from lake sediment was dependent on low temperatures (ca. 5 degrees c). however, this temperature effect was abolished when excessive amounts of dissolved organic carbon (10 mm n-acetylglucosamine) were added. a psychrotrophic freshwater isolate of c. johnsonae was used to study the physiological versatility of this group. exponential growth rates were found to be dependent on the temperature t ... | 1982 | 16346146 |
| long-term changes in chemostat cultures of cytophaga johnsonae. | long-term studies with a gliding, heterotrophic bacterium, cytophaga johnsonae, were conducted in a glucose-limited chemostat at a high and a low dilution rate. to test the stability of the steady state during long-term experiments the following parameters were monitored: optical density, glucose concentration, glucose uptake potential, atp content of the cells, and plate counts on two different agar media. biomass remained relatively constant, although the observed changes could have been possi ... | 1983 | 16346411 |
| transient responses of glucose-limited cultures of cytophaga johnsonae to nutrient excess and starvation. | cells from glucose-limited chemostat cultures of cytophaga johnsonae were subjected to a sudden relaxation of substrate limitation by injecting the cells into fresh batch cultures. starvation experiments were carried out by injecting glucose-limited cells into batch cultures lacking glucose. transient responses of biomass, glucose uptake and mineralization, atp content, and viability on different agar media were monitored during these nutrient-shift experiments. cells reacted differently dependi ... | 1984 | 16346475 |
| decomposition studies in two central ontario lakes having surficial phs of 4.6 and 6.6. | the rates of cellulose breakdown, composition of detrital microflora, and density of bacterial populations were determined in the epilimnetic sediments and water columns of two poorly buffered, oligotrophic, canadian shield lakes having mean surficial phs of 4.6 (bat lake) and 6.6 (harp lake). the decomposition rate was significantly lower in oxic sediment of the acidified lake than of the circumneutral lake, but water column rates were almost identical in the two lakes. these results are explai ... | 1986 | 16347147 |
| alteration of a salt marsh bacterial community by fertilization with sewage sludge. | the effects of long-term fertilization with sewage sludge on the aerobic, chemoheterotrophic portion of a salt marsh bacterial community were examined. the study site in the great sippewissett marsh, cape cod, mass., consisted of experimental plots that were treated with different amounts of commercial sewage sludge fertilizer or with urea and phosphate. the number of cfus, percentage of mercury- and cadmium-resistant bacteria, and percentage of antibiotic-resistant bacteria were all increased i ... | 1986 | 16347183 |
| uptake and incorporation of thymidine by bacterial isolates from an upwelling environment. | thymidine uptake and incorporation by marine bacterial isolates from an upwelling environment were studied. of 17 isolates each from upwelled and downwelled water, 1 and 6 isolates, respectively, were found to be negative for [h]thymidine incorporation at a substrate concentration of 19 mum. strains lacking the ability to take up thymidine were not confined to one genus. the measurable rates of uptake and incorporation by the 34 isolates varied greatly. studies carried out using starved vibrio, ... | 1989 | 16347916 |
| hydrophobicity, adhesion, and surface-exposed proteins of gliding bacteria. | the cell surface hydrophobicities of a variety of aquatic and terrestrial gliding bacteria were measured by an assay of bacterial adherence to hydrocarbons (bath), hydrophobic interaction chromatography, and the salt aggregation test. the bacteria demonstrated a broad range of hydrophobicities. results among the three hydrophobicity assays performed on very hydrophilic strains were quite consistent. bacterial adhesion to glass did not correlate with any particular measure of surface hydrophobici ... | 1991 | 16348583 |
| enumeration and characterization of bacterial colonists of a submersed aquatic plant, eurasian watermilfoil (myriophyllum spicatum l.). | a simple procedure for enumerating and grouping the bacterial colonists of eurasian watermilfoil (myriophyllum spicatum l.) is described. colony characteristics of bacteria associated with m. spicatum were better defined and more stable on nutrient-poor, diluted nutrient broth agar than on high-nutrient media. acinetobacter, cytophaga, flavobacterium, moraxella, pseudomonas and/or alcaligenes, and vibrio/aeromonas spp., as well as two highly fastidious unidentified bacterial groups (gram-negativ ... | 1992 | 16348792 |
| characteristics of myxobacteria isolated from the surface of freshwater fish. | a study was made of 32 nonpathogenic myxobacterial isolates obtained from a variety of fish taken in the pacific northwest. morphological, cultural, biochemical, and serological studies were carried out on these strains. all were found to be members of the genus cytophaga. two myxobacterial strains pathogenic to fish were also included in this study for comparative purposes. these pathogenic organisms were found to be culturally and physiologically similar to some of the nonpathogenic strains. a ... | 1968 | 16349828 |
| the cytophaga group: a contribution to the biology of myxobacteria. | | 1942 | 16350082 |
| 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 |
| [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 |
| molecular microbial diversity of a soil sample and detection of ammonia oxidizers from cape evans, mcmurdo dry valley, antarctica. | the aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, cape evans, mcmurdo, antarctica by an ssu rdna gene library approach. our study by sequencing of clones from ssu rdna gene library approach revealed high diversity in the soil sample from antarctica. more than 50% of clones showed homology to cytophaga-flavobacterium-bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, thermus-deinococcus and high gc ... | 2007 | 16517136 |
| 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 |
| community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. | the bacterial community structure in the winter cover and pelagic zone of a high mountain lake was analyzed by in situ hybridization with fluorescently labeled rrna-targeted oligonucleotide probes. cells fixed on membrane filters were hybridized with a probe specific for the domain bacteria as well as with probes for the alpha, beta, and gamma subclasses of the class proteobacteria and the cytophaga-flavobacterium group. the fraction of bacteria detectable after hybridization with the bacterial ... | 1996 | 16535341 |
| morphological and compositional shifts in an experimental bacterial community influenced by protists with contrasting feeding modes. | in a two-stage continuous-flow system, we studied the impacts of different protozoan feeding modes on the morphology and taxonomic structure of mixed bacterial consortia, which were utilizing organic carbon released by a pure culture of a rhodomonas sp. grown on inorganic medium in the first stage of the system. two of three second stages operated in parallel were inoculated by a bacterivorous flagellate, bodo saltans, and an algivorous ciliate, urotricha furcata, respectively. the third vessel ... | 1997 | 16535515 |
| 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 |
| cytophaga columnaris (davis) in pure culture: a myxobacterium pathogenic to fish. | | 1945 | 16560903 |
| studies on nonfruiting myxobacteria: i. cytophaga johnsonae, n.sp., a chitin-decomposing myxobacterium. | | 1947 | 16561273 |
| 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 |
| purification and characterization of an extracellular, uracil specific ribonuclease from a bizionia species isolated from the marine environment of the sundarbans. | the first ribonuclease (rnase) from the cytophaga-flavobacterium-bacteroides phylum, dominant in the marine environment, and also from the first bizionia species isolated from the tropics was purified and characterized. extracellular rnase production occurred when the culture medium contained 5-7% (w/v) nacl. the 53.0 kda enzyme was purified 29 folds with a recovery of 4% and specific activity of 630unit/mg protein. the ph and temperature optima are 6.5 and 35 degrees c, respectively and the enz ... | 2008 | 16644192 |
| phylogenetic diversity of culturable bacteria from alpine permafrost in the tianshan mountains, northwestern china. | microbes have been discovered in permafrost sediments for nearly a century. however, microbiological analyses of alpine permafrost are very scarce. this study is a first attempt to describe the phylogenetic diversity of a culturable bacterial community isolated from alpine permafrost in the tianshan mountains in northwestern china. aerobic 2.5-6.0x10(5) cfu/gdw (cfu per 1 gram of dry weight) on modified pygv medium were recovered from alpine permafrost samples at 4 degrees c; among these, 91 bac ... | 2006 | 16690258 |
| bacterial community along a historic lake sediment core of ardley island, west antarctica. | the bacterial community in a historic lake sediment core of ardley island, antarctica, spanning approximately 1,600 years, was investigated by molecular approaches targeting the 16s rrna gene fragments. the cell number in each 1 cm layer of the sediment core was deduced through semi-quantification of the 16s rrna gene copies by quantitative competitive pcr (qc-pcr). it was found that the total bacterial numbers remained relatively stable along the entire 59 cm sediment core. denaturing gradient ... | 2006 | 16715185 |
| microbial community structure and dynamics in the largest natural french lake (lake bourget). | we investigated the dynamics and diversity of heterotrophic bacteria, autotrophic and heterotrophic flagellates, and ciliates from march to july 2002 in the surface waters (0-50 m) of lake bourget. the heterotrophic bacteria consisted mainly of "small" cocci, but filaments (>2 microm), commonly considered to be grazing-resistant forms under increased nanoflagellate grazing, were also detected. these elongated cells mainly belonged to the cytophaga-flavobacterium (cf) cluster, and were most abund ... | 2006 | 16733620 |
| [phylogenetic analysis of bacterial diversity in pacific arctic sediments]. | using pcr-dgge (denaturing gradient gel electrophoresis) methods, bacterial phylogenetic diversity in three pacific arctic sediment samples were investigated, taken from different depths in the range of 47 m to 3850 m. dgge profiles of different layers in the same sediment sample are not completely same. 16s rdna sequences corresponding to 50 excised bands from three sediment samples were analyzed and fell into seven lineages of the domain bacteria: alpha- beta-, gamma-, delta-, epsilon- proteob ... | 2006 | 16736572 |
| [phylogenetic diversity and cold-adaptive hydrolytic enzymes of culturable psychrophilic bacteria associated with sea ice from high latitude ocean, artic]. | the phylogenetic diversity of culturable psychrophilic bacteria associated with sea ice from high latitude sea (77 degrees 30'n - 81 degrees 12'n), canadian basin and greenland sea arctic, was investigated. a total of 37 psychrophilic strains were isolated using three different methods of ( i ) spread plate method: 100 microl of each dilution ice-melt sample was spreaded onto the surface of marine 2216 agar (difco laboratories, detroit, mi) and incubated for 2 to 6 weeks at 4 degrees c; ( ii ) b ... | 2006 | 16736573 |
| decomposition of cellulose by cytophaga. i. | | 1938 | 16746597 |
| 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 |
| microbial diversity of cold-seep sediments in sagami bay, japan, as determined by 16s rrna gene and lipid analyses. | microbial communities in calyptogena sediment and microbial mats of sagami bay, japan, were characterized using 16s rrna gene sequencing and lipid biomarker analysis. characterization of 16s rrna gene isolated from these samples suggested a predominance of bacterial phylotypes related to gammaproteobacteria (57-64%) and deltaproteobacteria (27-29%). the epsilonproteobacteria commonly found in cold seeps and hydrothermal vents were only detected in the microbial mat sample. significantly differen ... | 2006 | 16907757 |
| community composition and activity of prokaryotes associated to detrital particles in two contrasting lake ecosystems. | the composition, distribution and extracellular enzyme activities of bacteria attached to small (2-50 microm in size) transparent exopolymer and coomassie-stained proteinaceous particles (tep and csp) were examined in two lakes of different trophic status located in the massif central of france. tep concentrations (10(4)-10(6) particle per l) were significantly higher in the more productive lake and were significantly related to chlorophyll a concentrations. the majority of tep and csp were colo ... | 2006 | 16907758 |
| community structure of the bacteria associated with nodularia sp. (cyanobacteria) aggregates in the baltic sea. | the community structure of the bacteria associated with nodularia spumigena (mertens) cyanobacterial aggregates in the baltic sea was studied with temperature gradient gel electrophoresis (tgge), using a 16s rrna gene fragment as a target. various developmental stages of the aggregates and free-floating cyanobacterial filaments were sampled to reveal possible changes in associated microbial community structure during development and senescence of the aggregates. the microbial community structure ... | 2006 | 16944338 |
| quantifying substrate uptake by individual cells of marine bacterioplankton by catalyzed reporter deposition fluorescence in situ hybridization combined with microautoradiography. | catalyzed reporter deposition fluorescence in situ hybridization combined with microautoradiography (micro-card-fish) is increasingly being used to obtain qualitative information on substrate uptake by individual members of specific prokaryotic communities. here we evaluated the potential for using this approach quantitatively by relating the measured silver grain area around cells taking up (3)h-labeled leucine to bulk leucine uptake measurements. the increase in the silver grain area over time ... | 2006 | 16950912 |
| transfer of [flexibacter] sancti, [flexibacter] filiformis, [flexibacter] japonensis and [cytophaga] arvensicola to the genus chitinophaga and description of chitinophaga skermanii sp. nov. | analysis of the 16s rrna gene sequences of species currently assigned to the genus flexibacter has shown extensive intrageneric phylogenetic heterogeneity. it has been shown in previous studies that the species [flexibacter] sancti, [flexibacter] filiformis and [flexibacter] japonensis were most closely related to chitinophaga pinensis. in addition, [cytophaga] arvensicola and species of the genus terrimonas also clustered into this phylogenetic group. although the similarities of 16s rrna gene ... | 2006 | 16957125 |
| rhizosphere microbial activity during phytoremediation of diesel-contaminated soil. | to know microbial activity and diesel-removal efficiency influencing through plant roots, we examined the effect of the rhizosphere on phytoremediation of diesel-contaminated soils by alfalfa (medicago sativa l.). pots were treated with and without diesel and allowed to stabilize for 7 weeks, at which time four experimental/control groups were prepared: (1) planted diesel-contaminated soil, (2) unplanted diesel-contaminated soil, (3) planted uncontaminated soil, and (4) unplanted uncontaminated ... | 2006 | 17000542 |
| roseobacter and sar11 dominate microbial glucose uptake in coastal north sea waters. | bacterial assemblages in coastal pelagic environments are exposed to pronounced temporal and spatial fluctuations in the availability of monomeric substrates. little is known about the response of particular bacterial groups to such variability. we studied glucose incorporation at various concentrations (0.1-100 nm) by bacteria related to roseobacter, sar11, gammaproteobacteria and cytophaga-flavobacteria in coastal north sea waters in late winter and during a spring phytoplankton bloom dominate ... | 2006 | 17014500 |
| predominance of roseobacter, sulfitobacter, glaciecola and psychrobacter in seawater collected off ushuaia, argentina, sub-antarctica. | bacterial diversity in sub-antarctic seawater, collected off ushuaia, argentina, was examined using a culture independent approach. the composition of the 16s rrna gene libraries from seawater and seawater contaminated with the water soluble fraction of crude oil was statistically different (p value 0.001). in both libraries, clones representing the alphaproteobacteria, gammaproteobacteria, the cytophaga-flavobacterium-bacteroidetes group and unculturable bacteria were dominant. clones associate ... | 2007 | 17026513 |
| cardinium symbionts cause cytoplasmic incompatibility in spider mites. | intracellular symbiotic bacteria belonging to the cytophaga-flavobacterium-bacteroides lineage have recently been described and are widely distributed in arthropod species. the newly discovered bacteria, named cardinium sp, cause the expression of various reproductive alterations in their arthropod hosts, including cytoplasmic incompatibility (ci), induction of parthenogenesis and feminization of genetic males. we detected 16s ribosomal dna sequences similar to those of cardinium from seven popu ... | 2007 | 17035954 |
| diverse responses to uv-b radiation and repair mechanisms of bacteria isolated from high-altitude aquatic environments. | acinetobacter johnsonii a2 isolated from the natural community of laguna azul (andean mountains at 4,560 m above sea level), serratia marcescens mf42, pseudomonas sp. strain mf8 isolated from the planktonic community, and cytophaga sp. strain mf7 isolated from the benthic community from laguna pozuelos (andean puna at 3,600 m above sea level) were subjected to uv-b (3,931 j m-2) irradiation. in addition, a marine pseudomonas putida strain, 2idinh, and a second acinetobacter johnsonii strain, atc ... | 2006 | 17056692 |
| the evolution of the genetic code took place in an anaerobic environment. | we have compared orthologous proteins from an aerobic organism, cytophaga hutchinsonii, and from an obligate anaerobe, bacteroides thetaiotaomicron. this comparison allows us to define the oxyphobic ranks of amino acids, i.e. a scale of the relative sensitivity to oxygen of the amino acid residues. the oxyphobic index (oi), which can be simply obtained from the amino acids' oxyphobic ranks, can be associated to any protein and therefore to the genetic code, if the number of synonymous codons att ... | 2007 | 17078972 |
| biodegradation of nonylphenol in soil. | we investigated the effects of various factors (brij 30, brij 35, yeast extract, hydrogen peroxide and compost) on the aerobic degradation of nonylphenol (np) in soil and characterized the structure of the microbial community in that soil. residues of np were measured using gas chromatography-mass spectrometry (gc-ms) and a change of microbial communities was demonstrated using denaturing gradient gel electrophoresis (dgge). the results showed that taichung sandy clay loam had higher np degradat ... | 2007 | 17092543 |
| deciphering function and mechanism of calcium-binding proteins from their evolutionary imprints. | calcium-binding proteins regulate ion metabolism and vital signalling pathways in all living organisms. our aim is to rationalize the molecular basis of their function by studying their evolution using computational biology techniques. phylogenetic analysis is of primary importance for classifying cognate orthologs; profile hidden markov models (hmm) of individual subfamilies discern functionally relevant sites by conservation probability analysis; and 3-dimensional structures display the integr ... | 2006 | 17092580 |
| microbial community structure in moraine lakes and glacial meltwaters, mount everest. | the bacterial diversity and abundance in two moraine lakes and two glacial meltwaters (5140, 5152, 5800 and 6350 m above sea level, respectively) in the remote mount everest region were examined through 16s rrna gene clone library and flow cytometry approaches. in total, 247 clones were screened by rflp and 60 16s rrna gene sequences were obtained, belonging to the following groups: proteobacteria (8% alpha subdivision, 21% beta subdivision, and 1% gamma subdivision), cytophaga-flavobacteria-bac ... | 2006 | 17107422 |
| whole genome analysis of the marine bacteroidetes'gramella forsetii' reveals adaptations to degradation of polymeric organic matter. | members of the bacteroidetes, formerly known as the cytophaga-flavobacteria-bacteroides (cfb) phylum, are among the major taxa of marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). in addition, they have been shown to also represent a significant part of free-living microbial assemblages in nutrient-rich microenvironments. their abundance and distribution pattern in combination with enzymatic activity studies has led to the notion that o ... | 2006 | 17107561 |
| nitrifying bacterial communities in an aquaculture wastewater treatment system using fluorescence in situ hybridization (fish), 16s rrna gene cloning, and phylogenetic analysis. | aquaculture, especially shrimp farming, has played a major role in the growth of thailand's economy in recent years, as well as in many south east asian countries. however, the nutrient discharges from these activities have caused adverse impacts on the quality of the receiving waterways. in particular nitrogenous compounds, which may accumulate in aquaculture ponds, can be toxic to aquatic animals and cause environmental problems such as eutrophication. the mineralization process is well known, ... | 2007 | 17115448 |
| does the importance of the c-terminal residues in the maturation of rgpb from porphyromonas gingivalis reveal a novel mechanism for protein export in a subgroup of gram-negative bacteria? | the mature 507-residue rgpb protein belongs to an important class of extracellular outer membrane-associated proteases, the gingipains, from the oral pathogen porphyromonas gingivalis that has been shown to play a central role in the virulence of the organism. the c termini of these gingipains along with other outer membrane proteins from the organism share homologous sequences and have been suggested to function in attachment of these proteins to the outer membrane. in this report, we have crea ... | 2007 | 17142394 |
| origin of the bacterial set domain genes: vertical or horizontal? | the presence of supressor of variegation-enhanser of zeste-trithorax (set) domain genes in bacteria is a current paradigm for lateral genetic exchange between eukaryotes and prokaryotes. because a major function of set domain proteins is the chemical modification of chromatin and bacteria do not have chromatin, there is no apparent functional requirement for the existence of bacterial set domain genes. consequently, their finding in only a small fraction of pathogenic and symbiotic bacteria was ... | 2007 | 17148507 |
| separation of marine bacteria according to buoyant density by use of the density-dependent cell sorting method. | the purpose of this study was to test whether some phylogenetic groups of natural marine bacteria have unique buoyant densities that allow them to be separated by the density-dependent cell sorting (ddcs) method. we first concentrated a natural bacterial assemblage to collect sufficient numbers of cells. they were separated into three fractions by ddcs, and the community structure in each was clarified by fluorescence in situ hybridization. the cells of archaea tended to appear in the high-densi ... | 2007 | 17158617 |
| coral disease diagnostics: what's between a plague and a band? | recently, reports of coral disease have increased significantly across the world's tropical oceans. despite increasing efforts to understand the changing incidence of coral disease, very few primary pathogens have been identified, and most studies remain dependent on the external appearance of corals for diagnosis. given this situation, our current understanding of coral disease and the progression and underlying causes thereof is very limited. in the present study, we use structural and microbi ... | 2007 | 17158622 |