| saccamoeba lacustris, sp. nov. (amoebozoa: lobosea: hartmannellidae), a new lobose amoeba, parasitized by the novel chlamydia 'candidatus metachlamydia lacustris' (chlamydiae: parachlamydiaceae). | an amoeba isolated from an aquatic biotope, identified morphologically as saccamoeba limax, was found harbouring mutualistic rod-shaped gram-negative bacteria. during their cultivation on agar plates, a coinfection also by lysis-inducing chlamydia-like organisms was found in some subpopulations of that amoeba. .here we provide a molecular-based identification of both the amoeba host and the two bacterial endosymbionts. analysis of the 18s rrna gene revealed that this strain is the sister-group t ... | 2010 | 20347279 |
| effects of plant genotype and growth stage on the betaproteobacterial communities associated with different potato cultivars in two fields. | bacterial communities in the rhizosphere are dynamic and susceptible to changes in plant conditions. among the bacteria, the betaproteobacteria play key roles in nutrient cycling and plant growth promotion, and hence the dynamics of their community structures in the rhizosphere should be investigated. here, the effects of plant cultivar, growth stage, and soil type on the communities associated with potato cultivars aveka, aventra, karnico, modena, premiere, and désirée were assessed for two dif ... | 2010 | 20363788 |
| assessment of mtbe biodegradation pathways by two-dimensional isotope analysis in mixed bacterial consortia under different redox conditions. | the fuel oxygenate, methyl tert-butyl ether (mtbe), although now widely banned or substituted, remains a persistent groundwater contaminant. multidimensional compound-specific isotope analysis (csia) of carbon and hydrogen is being developed for determining the extent of mtbe loss due to biodegradation and can also potentially distinguish between different biodegradation pathways. carbon and hydrogen isotopic fractionation factors were determined for mtbe degradation in aerobic and anaerobic lab ... | 2010 | 20582586 |
| mineralisation of the herbicide linuron by variovorax sp. strain ra8 isolated from japanese river sediment using an ecosystem model (microcosm). | linuron is a globally used phenylurea herbicide, and a large number of studies have been made on the microbial degradation of the herbicide. however, to date, the few bacteria able individually to mineralise linuron have been isolated only from european agricultural soils. an attempt was made to isolate linuron-mineralising bacteria from japanese river sediment using a uniquely designed river ecosystem model (microcosm) treated with (14)c-ring-labelled linuron (approximately 1 mg l(-1)). | 2010 | 20603879 |
| bacteria from drinking water supply and their fate in gastrointestinal tracts of germ-free mice: a phylogenetic comparison study. | microorganisms in drinking water sources may colonize in gastrointestinal (gi) tracts and this phenomenon may pose a potential health risk especially to immunocompromised population. the microbial community diversity of the drinking water was compared with the gi tracts of the mice using phylogenetic and statistical analyses of 16s rrna gene sequences. a group of germ-free mice were fed with drinking water from public water supply that passed through an automated watering system with documented ... | 2010 | 20705313 |
| evaluation of bioaugmentation with entrapped degrading cells as a soil remediation technology. | soil augmentation with microbial degraders immobilized on carriers is evaluated as a potential remediation technology using a mathematical model that includes degradation within spatially distributed carriers and diffusion or advection-dispersion as contaminant mass transfer mechanisms. the total volume of carriers is a critical parameter affecting biodegradation performance. in the absence of advection, 320 and 20 000 days are required to mineralize 90% of the herbicide linuron by variovorax sp ... | 2010 | 20812719 |
| aerobic degradation of mercaptosuccinate by the gram-negative bacterium variovorax paradoxus strain b4. | the gram-negative bacterium variovorax paradoxus strain b4 was isolated from soil under mesophilic and aerobic conditions to elucidate the so far unknown catabolism of mercaptosuccinate (ms). during growth with ms this strain released significant amounts of sulfate into the medium. tn5::mob-induced mutagenesis was successfully employed and yielded nine independent mutants incapable of using ms as a carbon source. in six of these mutants, tn5::mob insertions were mapped in a putative gene encodin ... | 2010 | 21075928 |
| complete genome sequence of the metabolically versatile plant growth-promoting endophyte variovorax paradoxus s110. | variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. v. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. the complete genome sequence of v. paradoxus s110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. genomic analysis has revealed multiple metabolic features f ... | 2010 | 21183664 |
| a molecular toolbox to estimate the number and diversity of variovorax in the environment: application in soils treated with the phenylurea herbicide linuron. | real-time pcr and pcr-denaturing gradient gel electrophoresis (dgge) approaches that specifically target the variovorax 16s rrna gene were developed to estimate the number and diversity of variovorax in environmental ecosystems. pcr primers suitable for both methods were selected as such that the enclosed sequence showed maximum polymorphism. pcr specificity was maximized by combining pcr with a targeted endonuclease treatment of template dna to eliminate 16s rrna genes of the closely related ac ... | 2011 | 21204875 |
| isolation and identification of soil bacteria growing at the expense of arbuscular mycorrhizal fungi. | soil-microorganism symbioses are of fundamental importance for plant adaptation to the environment. research in microbial ecology has revealed that some soil bacteria are associated with arbuscular mycorrhizal fungi (amf). however, these interactions may be much more complex than originally thought. to assess the type of bacteria associated with amf, we initially isolated spores of glomus irregulare from an agrostis stolonifera rhizosphere. the spores were washed with sterile water and plated on ... | 2011 | 21219415 |
| improvement of pesticide mineralization in on-farm biopurification systems by bioaugmentation with pesticide-primed soil. | microcosms were used to examine whether pesticide-primed soils could be preferentially used over nonprimed soils for bioaugmentation of on-farm biopurification systems (bps) to improve pesticide mineralization. microcosms containing a mixture of peat, straw and either linuron-primed soil or nonprimed soil were irrigated with clean or linuron-contaminated water. the lag time of linuron mineralization, recorded for microcosm samples, was indicative of the dynamics of the linuron-mineralizing bioma ... | 2011 | 21231937 |
| relative quantitative pcr to assess bacterial community dynamics during biodegradation of diesel and biodiesel fuels under various aeration conditions. | the degradation of diesel fuel, b20 blend and biodiesel in liquid cultures by a seven-member bacterial consortium was compared under conditions with full aeration or with limited aeration with nitrate added as main electron acceptor. community dynamics was assessed employing real-time pcr and the ddct method for relative quantification. biodegradation rates increased with increasing biodiesel content, but were significantly reduced under conditions with nitrate. despite large variations in biode ... | 2010 | 21239170 |
| effects of the antimicrobial sulfamethoxazole on groundwater bacterial enrichment. | the effects of "trace" (environmentally relevant) concentrations of the antimicrobial agent sulfamethoxazole (smx) on the growth, nitrate reduction activity, and bacterial composition of an enrichment culture prepared with groundwater from a pristine zone of a sandy drinking-water aquifer on cape cod, ma, were assessed by laboratory incubations. when the enrichments were grown under heterotrophic denitrifying conditions and exposed to smx, noticeable differences from the control (no smx) were ob ... | 2011 | 21384910 |
| multiple dna extractions coupled with stable-isotope probing of anthracene-degrading bacteria in contaminated soil. | in many of the dna-based stable-isotope probing (sip) studies published to date in which soil communities were investigated, a single dna extraction was performed on the soil sample, usually using a commercial dna extraction kit, prior to recovering the (13)c-labeled (heavy) dna by density-gradient ultracentrifugation. recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of dna from all of the organisms in the sample. to determine w ... | 2011 | 21398486 |
| aerobic cometabolism of trichloroethene and cis-dichloroethene with benzene and chlorinated benzenes as growth substrates. | using inoculum from a microcosm study that exhibited aerobic transformation of cis-1,2-dichloroethene (cdce) and trichloroethene (tce) commensurate with biodegradation of monoaromatic compounds, enrichment cultures were developed by providing benzene, chlorobenzene (cb), dichlorobenzene (dcb) isomers and 1,2,4-trichlorobenzene as carbon and energy sources. isolates that grow on benzene, cb, 1,2-dcb and 1,3-dcb were identified as rhodococcus, ralstonia, variovorax and ralstonia spp., respectively ... | 2011 | 21531438 |
| molecular definition of vaginal microbiota in east african commercial sex workers. | resistance to hiv infection in a cohort of commercial sex workers (csw) living in nairobi, kenya is linked to mucosal and anti-inflammatory factors that may be influenced by vaginal microbiota. since bacterial vaginosis (bv), a polymicrobial dysbiosis characterized by low levels of protective lactobacillus organisms, is an established risk factor for hiv infection, we investigated whether vaginal microbiology was associated with hiv-exposed seronegative (hesn) or hiv-seropositive (hiv+) status i ... | 2011 | 21531840 |
| [diversity of siderophore-producing endophytic bacteria of cymbidium goeringii roots]. | in order to obtain the effective plant growth-promoting bacteria, we studied the diversity of siderophore-producing endophytic bacteria in the roots of cymbidium goeringii. | 2011 | 21574379 |
| culturable bacterial community analysis in the root domains of two different tree peony (paeonia ostii) variety plants. | a total of 985 bacterial strains with different colony characteristics were isolated from the root of tree peony plants (variety 'fengdan' and 'lan furong'), which were 69 otus identified by ardra. representatives of each group were selected for partial 16s rrna gene sequencing and phylogenetic analysis. the major group in the bulk soil, rhizosphere and rhizoplane of 'fengdan' were firmicutes (63.2%), actinobacteria (36.3%) and betaproteobacteria (53.0%), respectively. while the major bacteria g ... | 2011 | 21623895 |
| robust linuron degradation in on-farm biopurification systems exposed to sequential environmental changes. | on-farm biopurification systems (bps) treat pesticide-contaminated waste water of farms through biodegradation. adding pesticide-primed soil has been shown to be beneficial for the establishment of pesticide-degrading populations in bps. however, no data exist on the response of pesticide-degrading microbiota, either endogenous or introduced with pesticide-primed soil, when bps are exposed to expected less favorable environmental conditions like cold periods, drought periods and periods without ... | 2011 | 21803897 |
| biotransformation of the neonicotinoid insecticide thiacloprid by the bacterium variovorax boronicumulans strain j1 and mediation of the major metabolic pathway by nitrile hydratase. | a neonicotinoid insecticide thiacloprid-degrading bacterium strain j1 was isolated from soil and identified as variovorax boronicumulans by 16s rrna gene sequence analysis. liquid chromatography-mass spectrometry and nuclear magnetic resonance analysis indicated the major pathway of thiacloprid (thi) metabolism by v. boronicumulans j1 involved hydrolysis of the n-cyanoimino group to form an n-carbamoylinino group containing metabolite, thi amide. resting cells of v. boronicumulans j1 degraded ... | 2011 | 22148554 |
| comparative geochemical and microbiological characterization of two thermal pools in the uzon caldera, kamchatka, russia. | arkashin schurf (arkashin) and zavarzin spring (zavarzin), two active thermal pools in the uzon caldera, kamchatka, russia, were studied for geochemical and microbiological characterization. arkashin, the smaller of the two pools, had broader temperature and ph ranges, and the sediments had higher concentrations of total as (4,250 mg/kg) relative to zavarzin (48.9 mg/kg). glycerol dialkyl glycerol tetraether profiles represented distinct archaeal communities in each pool and agreed well with pre ... | 2011 | 22124570 |
| a novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by variovorax sp. strain srs16. | the soil bacterial isolate variovorax sp. strain srs16 mineralizes the phenylurea herbicide linuron. the proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (dca) and n,o-dimethylhydroxylamine, followed by conversion of dca to krebs cycle intermediates. differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (liba), a multicomponent chloroaniline dioxygenase, and enzymes associated with a ... | 2011 | 22003008 |
| High-sensitivity stable-isotope probing by a quantitative terminal restriction fragment length polymorphism protocol. | Stable-isotope probing (SIP) has proved a valuable cultivation-independent tool for linking specific microbial populations to selected functions in various natural and engineered systems. However, application of SIP to microbial populations with relatively minor buoyant density increases, such as populations that utilize compounds as a nitrogen source, results in reduced resolution of labeled populations. We therefore developed a tandem quantitative PCR (qPCR)-TRFLP (terminal restriction fragmen ... | 2012 | 22038597 |
| variovorax defluvii sp. nov., isolated from sewage flowing into river geumho in south korea. | a polyphasic taxonomic study was carried out on 2c1-b(t) and 2c-21, two strains isolated from the sewage flowing into river geumho in korea.the cells of strains were gram-negative, non-spore-forming, motile and oval or rod-shaped bacteria. comparative 16s rrna gene sequence studies showed a clear affiliation of these two bacteria into the betaproteobacteria, which were most closely related to variovorax boronicumulans kctc 22010(t), variovorax dokdonensis kctc 12544(t), variovorax ginsengisoli k ... | 2011 | 21948092 |
| Isolation of bacteria capable of growth with 2-methylisoborneol and geosmin as the sole carbon and energy sources. | Using a relatively simple enrichment technique, geosmin and 2-methylisoborneol (MIB)-biodegrading bacteria were isolated from a digestion basin in an aquaculture unit. Comparison of 16S rRNA gene sequences affiliated one of the three isolates with the Gram-positive genus Rhodococcus, while the other two isolates were found to be closely related to the Gram-negative family Comamonadaceae (Variovorax and Comamonas). Growth rates and geosmin and MIB removal rates by the isolates were determined und ... | 2012 | 22081577 |
| biodiversity characterization of cellulolytic bacteria present on native chaco soil by comparison of ribosomal rna genes. | sequence analysis of the 16s ribosomal rna gene was used to study bacterial diversity of a pristine forest soil and of two cultures of the same soil enriched with cellulolytic bacteria. our analysis revealed high bacterial diversity in the native soil sample, evidencing at least 10 phyla, in which actinobacteria, proteobacteria and acidobacteria accounted for more than 76% of all sequences. in both enriched samples, members of proteobacteria were the most frequently represented. the majority of ... | 2011 | 22202170 |
| Bacterial communities in urban aerosols collected with wetted-wall cyclonic samplers and seasonal fluctuations of live and culturable airborne bacteria. | Airborne transmission of bacterial pathogens from point sources (e.g., ranches, dairy waste treatment facilities) to areas of food production (farms) has been suspected. Determining the incidence, transport and viability of extremely low levels of pathogens require collection of high volumes of air and characterization of live bacteria from aerosols. We monitored the numbers of culturable bacteria in urban aerosols on 21 separate days during a 9 month period using high volume cyclonic samplers a ... | 2011 | 22193549 |