| performances and microbial features of a granular activated carbon packed-bed biofilm reactor capable of an efficient anaerobic digestion of olive mill wastewaters. | anaerobic digestion of olive mill wastewaters is generally performed in anaerobic contact bioreactors where the removal of toxic phenols is often unsatisfactory. in the present work we show that a granular activated carbon packed-bed biofilm reactor can be successfully used to achieve effective and reproducible wastewater decontamination even at high organic loads. a comparison of 16s rrna gene sequences of the inoculum and of biomass samples from different districts of the reactor revealed enri ... | 2004 | 19712310 |
| phylogenetic diversity of bacteria associated with paleolithic paintings and surrounding rock walls in two spanish caves (llonín and la garma). | bacterial diversity in caves is still rarely investigated using culture-independent techniques. in the present study, bacterial communities on paleolithic paintings and surrounding rock walls in two spanish caves (llonín and la garma) were analyzed, using 16s rdna-based denaturing gradient gel electrophoresis community fingerprinting and phylogenetic analyses without prior cultivation. results revealed complex bacterial communities consisting of a high number of novel 16s rdna sequence types and ... | 2004 | 19712338 |
| phylogenetic diversity of bacteria in the leachate of a full-scale recirculating landfill. | we analyzed the phylogenetic composition of bacterial community in the effluent leachate of a full-scale recirculating landfill using a culture-independent molecular approach. 16s rrna genes were amplified directly from leachate dna with universally conserved and bacteria-specific rdna primers and cloned. the clone library was screened by restriction fragment length polymorphism, and representative rdna sequences were determined. many bacterial sequences displaying relatively low levels of simil ... | 2004 | 19712358 |
| identification of rice root associated nitrate, sulfate and ferric iron reducing bacteria during root decomposition. | leakage of o(2) from roots of aquatic plants supports the oxidation of ammonia to nitrate and of sulfide to sulfate in the rhizosphere, so that these electron acceptors may become available to the root microbial communities and affect their activity. we studied the composition of the bacterial community active in anoxically incubated rice roots by analysis of terminal restriction fragment length polymorphism (t-rflp) and by cloning and sequencing targeting bacterial 16s rrna. the bacterial ribos ... | 2004 | 19712368 |
| distribution of prokaryotic genetic diversity in athalassohaline lakes of the atacama desert, northern chile. | athalassohaline lakes are inland saline aquatic environments with ionic proportions quite different from the dissolved salts in seawater. prokaryotes inhabiting athalassohaline environments are poorly known and very few of such places have been surveyed for microbial diversity studies around the world. we analyzed the planktonic bacterial and archaeal assemblages inhabiting several of these evaporitic basins in a remote and vast area in northern chile by pcr-denaturing gradient gel electrophores ... | 2004 | 19712431 |
| effects of copper amendment on the bacterial community in agricultural soil analyzed by the t-rflp technique. | abstract the impact of copper amendment on the bacterial community in agricultural soil was investigated by a 2-year field experiment complemented by short-term microcosm studies. in the field, the amendments led to total copper contents that were close to the safety limits laid down by european authorities. in parallel, bioavailable copper was determined with a copper-specific bioluminescent pseudomonas reporter strain. the amounts of total cu as well as of bioavailable cu in the field declined ... | 2003 | 19719582 |
| isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a sphagnum peat bog. | two dense and highly enriched (up to 10(9) cells ml(-1), <10% of bacterial satellites) acido-tolerant (ph 4.0-6.5) methanogenic consortia, '26' and 'k', were isolated from the peat beneath a sphagnum-eriophorum-carex community in west siberia. both consortia produced methane from co2:h2 on chemically defined, diluted n-free media containing ti(iii)citrate as reducing agent. the phylogenetic analysis of 16s ribosomal dna revealed three archaeal and nine bacterial sequence types. consortium '26' c ... | 2003 | 19719599 |
| bacterioplankton community diversity in a maritime antarctic lake, determined by culture-dependent and culture-independent techniques. | abstract the biodiversity of the pelagic bacterioplankton community of a maritime antarctic freshwater lake was examined by cultivation-dependent and cultivation-independent techniques to determine predominant bacterioplankton populations present. the culture-dependent techniques used were direct culture and observation, polymerase chain reaction amplification of 16s rrna gene fragments, restriction fragment length polymorphism (rflp) analysis followed by selective sequencing and fatty acid meth ... | 2003 | 19719607 |
| bacteria associated with sardine (sardina pilchardus) eggs in a natural environment (ría de vigo, galicia, northwestern spain). | abstract the present study was undertaken to describe the epiflora of the eggs of an important fishing species collected in a coastal zone. microflora associated with sardine (sardina pilchardus) eggs collected in the ría de vigo was examined from january to june 2000. the count was carried out in three different ways: a total direct count by epifluorescence, a heterotrophic bacteria count on marine agar (ma) and a total vibrio count on thiosulfate citrate bile sucrose (tcbs). it was observed th ... | 2003 | 19719614 |
| salinity as a structuring factor for the composition and performance of bacterioplankton degrading riverine doc. | abstract the impact of salinity on the composition and functional performance (biomass production, growth efficiency and growth rates) of bacterial communities was investigated using batch cultures growing on dissolved organic carbon from a river draining into the northern baltic sea. the cultures were adjusted to riverine or estuarine salinity levels and inoculated with bacteria from these two environments. bacterial growth efficiencies differed in response to salinity and the origin of the ino ... | 2003 | 19719630 |
| design and evaluation of group-specific oligonucleotide probes for quantitative analysis of intestinal ecosystems: their application to assessment of equine colonic microflora. | nine oligonucleotide probes complementary to conserved regions of small subunit rrna from phylogenetically defined clusters of intestinal anaerobic bacteria were designed and evaluated for use in quantitative analysis of intestinal microflora. optimum wash temperatures (t(w)) were determined according to the temperature of dissociation (t(d)) of each probe and target group specificity was demonstrated by comparing hybridisation to target and non-target rrna immobilised on nylon membranes. three ... | 2003 | 19719641 |
| activity and distribution of bacterial populations in middle atlantic bight shelf sands. | abstract spatiotemporal variation and metabolic activity of the microbial community were studied in coarse-grained middle atlantic bight shelf sediments in relation to pools of dissolved and particulate carbon. algal cells were present 8->70 mum) fraction of the sediment held the major share (61-98%) of benthic bacteria. bacterial and algal cell abundances, exoenzymatic activity, and [doc] generally showed higher values in may/july 2001 than in august/december 2000. carbohydrates and proteins we ... | 2003 | 19719654 |
| molecular sequence analysis of prokaryotic diversity in the anoxic sediments underlying cyanobacterial mats of two hypersaline ponds in mediterranean salterns. | abstract small-subunit (16s) ribosomal dna clone libraries were constructed using dna isolated from the anoxic sediments underlying the cyanobacterial mats from two sampling stations of different salinity (station a, 150-200 per thousand salinity; station b, 250-320 per thousand salinity) located in the mediterranean salterns of salin-de-giraud (france). previous studies have shown that the mats at these two sites differ greatly in physicochemical and microbial composition. sequence analysis of ... | 2003 | 19719657 |
| bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescent in situ hybridization and dgge analysis. | abstract physiologic activity and community structure of planktonic and biofilm microbial communities in an urban river were analyzed using 5-cyano-2,3-ditolyl tetrazolium chloride (ctc) staining, fluorescent in situ hybridization (fish) and denaturing gradient gel electrophoresis (dgge) analysis of polymerase chain reaction (pcr)-amplified 16s rdna fragments. respiring bacteria estimated by ctc reduction were higher in biofilms (20%) than in stream water samples (12%). fish analysis revealed th ... | 2003 | 19719701 |
| prevalence of cardinium bacteria in planthoppers and spider mites and taxonomic revision of "candidatus cardinium hertigii" based on detection of a new cardinium group from biting midges. | cardinium bacteria, members of the phylum cytophaga-flavobacterium-bacteroides (cfb), are intracellular bacteria in arthropods that are capable of inducing reproductive abnormalities in their hosts, which include parasitic wasps, mites, and spiders. a high frequency of cardinium infection was detected in planthoppers (27 out of 57 species were infected). a high frequency of cardinium infection was also found in spider mites (9 out of 22 species were infected). frequencies of double infection by ... | 2009 | 19734338 |
| phylogenetic analysis of 16s rrna gene sequences reveals rumen bacterial diversity in yaks (bos grunniens). | six matured male yaks (bos grunniens) with a mean live weight of 450 +/- 23 kg (mean +/- sd), were housed indoors in metabolism cages and fed pelleted lucerne (medicago sativum). after an adjustment period of 24 days of feeding the diet, samples of rumen content were obtained for analysis of the bacteria in the liquor. the diversity of rumen bacteria was investigated by constructing a 16s rrna gene clone library using the general bacterial primers f27 and r1492. a total of 130 clones, comprising ... | 2010 | 19757178 |
| the cytophaga hutchinsonii chtpsp: first characterized bifunctional tps-tpp protein as putative ancestor of all eukaryotic trehalose biosynthesis proteins. | the most widely distributed pathway to synthesize trehalose in nature consists of two consecutive enzymatic reactions with a trehalose-6-p (t6p)-synthase (tps) enzyme, producing the intermediate t6p, and a t6p-phosphatase (tpp) enzyme, which dephosphorylates t6p to produce trehalose and inorganic phosphate. in plants, these enzymes are called class i and class ii proteins, respectively, with some class i proteins being active enzymes. the class ii proteins possess both tps and tpp consensus regi ... | 2010 | 19812028 |
| bacterial populations in epilithic biofilms along two oligotrophic rivers in the tohoku region in japan. | bacterial populations in epilithic biofilms collected from two distinct oligotrophic rivers of japan were studied using denaturing gradient gel electrophoresis (dgge). pcr-dgge of the 16s rrna gene and subsequent sequencing analysis suggested that in freshwater biofilms, members of the cytophaga-flavobacterium-bacteroides (cfb) group were the most dominant, followed by those of alpha, beta, gamma, and delta-proteobacteria; leptospiraceae; and unidentified bacteria. members of the cfb group, alph ... | 2009 | 19940382 |
| stability of partial nitrification and microbial population dynamics in a bioaugmented membrane bioreactor. | bioaugmentation of bioreactors focuses on the removal of numerous organics, with little attention typically paid to the maintenance of high and stable nitrite accumulation in partial nitrification. in this study, a bioaugmented membrane bioreactor (mbr) inoculated with enriched ammonia-oxidizing bacteria (aob) was developed, and the effects of dissolved oxygen (do) and temperature on stability of partial nitrification and microbial community structure, in particular on nitrifying community were ... | 2009 | 20075634 |
| the uronic acids assay: a method for the determination of chemical activity on biofilm eps. | in this work, the uronic acids assay was evaluated for its potential to function as a bioassay to screen for antagonistic activity against the production of microbial biofilm exopolysaccharide (eps). the assay was first applied to biofilms produced in the presence of two universal disinfectants (sodium hypochlorite and sodium dodecyl sulfate) known to inhibit microbial growth and biofilm formation. the performance of the assay was then characterized through statistical assessment of threshold co ... | 2010 | 20087802 |
| the effects of n:p ratio and nitrogen form on four major freshwater bacterial taxa in biofilms. | bacteria in freshwater systems play an important role in nutrient cycling through both assimilatory and dissimilatory processes. biotic and abiotic components of the environment affect these transformations as does the stoichiometry of the nutrients. we examined responses of four major taxa of bacteria in biofilms subjected to various n:p molar ratios using either nitrate or ammonium as a nitrogen source. fluorescent in situ hybridization was used to enumerate the domain bacteria as well as the ... | 2010 | 20130692 |
| acylhomoserine lactone production and degradation by the fish pathogen tenacibaculum maritimum, a member of the cytophaga-flavobacterium-bacteroides (cfb) group. | abstract tenacibaculum maritimum (formerly flexibacter maritimus) is a filamentous, biofilm-forming member of the cytophaga-flavobacterium-bacteroides group (or bacteroidetes), which causes the widely distributed marine fish disease tenacibaculosis. a search for n-acylhomoserine lactones (ahls) quorum-sensing (qs) signals in the culture media of nine representative strains of this species using different biosensor strains revealed the presence of short-type ahl activity in all of them. n-butyryl ... | 2010 | 20132308 |
| studies on nonfruiting myxobacteria; cytophaga johnsonae, n. sp., a chitindecomposing myxobacterium. | | 1947 | 20290967 |
| changes in epiphytic bacterial communities of intertidal seaweeds modulated by host, temporality, and copper enrichment. | this study reports on the factors involved in regulating the composition and structure of bacterial communities epiphytic on intertidal macroalgae, exploring their temporal variability and the role of copper pollution. culture-independent, molecular approaches were chosen for this purpose and three host species were used as models: the ephemeral ulva spp. (chlorophyceae) and scytosiphon lomentaria (phaeophyceae) and the long-living lessonia nigrescens (phaeophyceae). the algae were collected fro ... | 2010 | 20333374 |
| cellulose and cellodextrin utilization by the cellulolytic bacterium cytophaga hutchisonii. | cytophaga hutchinsonii is an abundant aerobic cellulolytic soil bacterium utilizing very few substrates as sole carbon and energy sources. in this study, growth of c. hutchinsonii on different substrates including crystalline cellulose, regenerated amorphous cellulose (rac) as well as soluble sugars including cellodextrins was analyzed. soluble sugars including glucose and cellodextrins were produced extracellularly when c. hutchinsonii was cultured on cellulose. preferential use of cellulooligo ... | 2010 | 20362433 |
| acylhomoserine lactone production and degradation by the fish pathogen tenacibaculum maritimum, a member of the cytophaga-flavobacterium-bacteroides (cfb) group. | tenacibaculum maritimum (formerly flexibacter maritimus) is a filamentous, biofilm-forming member of the cytophaga-flavobacterium-bacteroides group (or bacteroidetes), which causes the widely distributed marine fish disease tenacibaculosis. a search for n-acylhomoserine lactones (ahls) quorum-sensing (qs) signals in the culture media of nine representative strains of this species using different biosensor strains revealed the presence of short-type ahl activity in all of them. n-butyryl-l-homose ... | 2010 | 20377642 |
| microbial dynamics in upflow anaerobic sludge blanket (uasb) bioreactor granules in response to short-term changes in substrate feed. | the upflow anaerobic sludge blanket (uasb) reactor is a microcosm for the methanogenic degradation of organic matter in anaerobic environments, and depends on the auto-formation of dense 3d biofilms of 1-3 mm in diameter, referred to as granular sludge (biogranules). past research has shown that uasb and other methanogenic reactors are extremely stable functionally, but the underlying basis of the functional stability is not well understood. in this study, microbial dynamics in the communities r ... | 2010 | 20430810 |
| seasonal succession and uv sensitivity of marine bacterioplankton at an antarctic coastal site. | despite extensive microbial biodiversity studies around the globe, studies focusing on diversity and community composition of bacteria in antarctic coastal regions are still scarce. here, we studied the diversity and development of bacterioplankton communities from prydz bay (eastern antarctic) during spring and early summer 2002-2003. additionally, we investigated the possible shaping effects of solar uv radiation (uv-r: 280-400 nm) on bacterioplankton communities incubated for 13-14 days in 65 ... | 2010 | 20455939 |
| impact of pollution and seasonal changes on microbial community structure in surface water. | we studied the differences in a microbial community structure with respect to the water pollution level and seasonal changes. the determination of phylogenetic groups of bacteria and archaea was done using fluorescent in situ hybridization (fish). the total number of microorganisms was determined by direct counting of dapi (4',6-diamidino-2-phenylindole) stained samples using a fluorescence microscope. our results showed that the microbial community structure was significantly dependent on the l ... | 2010 | 20489251 |
| endophytic bacterial diversity in roots of phragmites australis in constructed beijing cuihu wetland (china). | the community structure and diversity of endophytic bacteria in reed (phragmites australis) roots growing in the beijing cuihu wetland, china was investigated using the 16s rrna library technique. primers 799f and 1492r were used to amplify the specific bacterial 16s rrna fragments successfully and construct the clone library. in total, 166 individual sequences were verified by colony pcr and used to assess the diversity of endophytic bacteria in reed roots. phylogenetic analysis revealed that 7 ... | 2010 | 20528944 |
| ultraviolet radiation induces filamentation in bacterial assemblages from north andean patagonian lakes. | through laboratory experiments, we tested whether uv radiation (uvr) induces filamentation in natural bacteria assemblages from north andean patagonian lakes. we incubated water from three different lakes for 72 h in four separate treatments: (1) uvr + par (photosynthetically active radiation), (2) 50% uvr + par, (3) par and (4) 50% par. the irradiance levels used in the experiments were equivalent to those registered at the epilimnion of the lakes. in the uvr treatments filamentation was induce ... | 2010 | 20528974 |
| alteration of microbial communities colonizing leaf litter in a temperate woodland stream by growth of trees under conditions of elevated atmospheric co2. | elevated atmospheric co(2) can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. this study test ... | 2010 | 20543045 |
| distribution and diversity of bacteria in a saline meromictic lake as determined by pcr-dgge of 16s rrna gene fragments. | the variations in vertical distribution and composition of bacteria in the meromictic lake faro (messina, italy) were analysed by culture-independent methods in two different mixing conditions. water samples were collected from a central station from the surface to the bottom (30 m depth) on two different sampling dates--the first characterised by a well-mixed water mass and the second by a marked stratification. a 'red-water' layer, caused by a dense growth of photosynthetic sulphur bacteria, w ... | 2011 | 20544199 |
| abundance and diversity of heterotrophic bacterial cells assimilating phosphate in the subtropical north atlantic ocean. | microorganisms play key roles in the cycles of carbon and nutrients in the ocean, and identifying the extent to which specific taxa contribute to these cycles will establish their ecological function. we examined the use of (33)p-phosphate to identify heterotrophic bacteria actively involved in the cycling of phosphate, an essential inorganic nutrient. seawater from the sub-tropical north atlantic ocean was incubated with (33)p-phosphate and analysed by microautoradiography to determine the prop ... | 2010 | 20545744 |
| diversity and abundance of the bacterial 16s rrna gene sequences in forestomach of alpacas (lama pacos) and sheep (ovis aries). | two bacterial 16s rrna gene clone libraries were constructed from the forestomach of alpacas and sheep fed alfalfa. after the amplification using the universal 16s rrna gene primers, equal quantities of pcr products from the same species were mixed and used to construct the two libraries. sequence analysis showed that the 60 clones from alpacas were divided into 27 phylotypes with 25% clones affiliated with eubacterium sp. f1. the 60 clones from sheep were divided into 21 phylotypes with 7 phylo ... | 2010 | 20558310 |
| mining dictyoglomus turgidum for enzymatically active carbohydrases. | the genome of dictyoglomus turgidum was sequenced and analyzed for carbohydrases. the broad range of carbohydrate substrate utilization is reflected in the high number of glycosyl hydrolases, 54, and the high percentage of cazymes present in the genome, 3.09% of its total genes. screening a random clone library generated from d. turgidum resulted in the discovery of five novel biomass-degrading enzymes with low homology to known molecules. whole genome sequencing of the organism followed by bioi ... | 2011 | 20635162 |
| bacterial activity and bacterioplankton diversity in the eutrophic river warnow--direct measurement of bacterial growth efficiency and its effect on carbon utilization. | the influence of bacterial activity and diversity on bacterial growth efficiency was investigated in a flatland river. eutrophic river warnow drains predominantly agricultural land and is heavily loaded with nutrients, dissolved and particulate organic matter (dom and pom), especially humic substances. although the water column bacterial community consists of many inactive or damaged cells, bacterioplankton sustained a high bacterial secondary production of 0.2-14.5 μg c l(-1) h(-1) and a high d ... | 2011 | 20676625 |
| seasonal patterns of the bacterioplankton community composition in a lake threatened by a pesticide disposal site. | background aim and scope: the objective of the study was to determine the effects of ca. 35 years of pesticide contamination (pesticide dump-pd) of lake szeląg wielki (located in the north-eastern poland) on changes in the microbial communities of aquatic ecosystems. in the years 2008-2009, analyses were carried out for seasonal changes in the quantity and composition of bacterioplankton in the lake examined, which is of high significance to the tourism and fishing industries and is located in t ... | 2011 | 20694834 |
| bacterial diversity in the rumen of indian surti buffalo (bubalus bubalis), assessed by 16s rdna analysis. | bacterial communities in buffalo rumen were characterized using a culture-independent approach for a pooled sample of rumen fluid from 3 adult surti buffaloes. buffalo rumen is likely to include species of various bacterial phyla, so 16s rdna sequences were amplified and cloned from the sample. a total of 191 clones were sequenced and similarities to known 16s rdna sequences were examined. about 62.82% sequences (120 clones) had >90% similarity to the 16s rdna database sequences. furthermore, ab ... | 2010 | 20720314 |
| reproductive fitness and dietary choice behavior of the genetic model organism caenorhabditis elegans under semi-natural conditions. | laboratory breeding conditions of the model organism c. elegans do not correspond with the conditions in its natural soil habitat. to assess the consequences of the differences in environmental conditions, the effects of air composition, medium and bacterial food on reproductive fitness and/or dietary-choice behavior of c. elegans were investigated. the reproductive fitness of c. elegans was maximal under oxygen deficiency and not influenced by a high fractional share of carbon dioxide. in media ... | 2010 | 20821059 |
| sulfate reduction, molecular diversity, and copper amendment effects in bacterial communities enriched from sediments exposed to copper mining residues. | sulfate-reducing bacterial communities from coastal sediments with a long-term exposure to copper (cu)-mining residues were studied in lactate enrichments. the toxicity of excess copper may affect sulfate-reducing bacterial communities. sulfate reduction was monitored by sulfate and organic acid measurements. molecular diversity was analyzed by 16s rrna, dissimilatory sulfate reduction dsrab, and cu translocating phospho-type adenosine triphosphatases (p-atpases) cop-like gene sequence profiling ... | 2010 | 20821443 |
| molecular analyses of the diversity in marine bacterioplankton assemblages along the coastline of the northeastern gulf of mexico. | bacterial community diversity in marine bacterioplankton assemblages were examined in 3 coastal locations along the northeastern gulf of mexico (gom) using 16s rrna gene libraries and fluorescence in situ hybridization approaches. the majority of the sequences (30%-60%) were similar to the 16s rrna gene sequences of unknown bacteria; however, the operational taxonomic units from members of the cyanobacteria, proteobacteria, and bacteroidetes were also present at the 3 gom sites. overall, sequenc ... | 2010 | 20962909 |
| analysis of the composition and characteristics of culturable endophytic bacteria within subnival plants of the tianshan mountains, northwestern china. | this study first described the composition and characteristics of culturable endophytic bacteria isolated from wild alpine-subnival plant species growing under extreme environmental conditions (i.e., on the border of a glacier with frequently fluctuating and freezing temperatures, strong wind, and high ultraviolet radiation). using a cultivation-dependent approach and 16s rrna gene amplification techniques, 93 bacterial isolates showing different phenotypic properties were obtained from 20 diffe ... | 2011 | 21061126 |
| assessing the activity and diversity of fumarate-fed denitrifying bacteria by performing field single-well push-pull tests. | in situ biological denitrification has been proposed as an important metabolic activity in the remediation of nitrate-contaminated groundwater. in this study, the effects of fumarate, an electron donor for biological denitrification, on the in situ denitrifying activity were determined by using three types of single-well push-pull tests; transport, biostimulation and activity tests. during the tests, changes in microbial community composition were also investigated using denaturing gradient gel ... | 2011 | 21104493 |
| endophytic bacterial diversity in roots of typha angustifolia l. in the constructed beijing cuihu wetland (china). | we investigated the community structure of endophytic bacteria in narrowleaf cattail (typha angustifolia l.) roots growing in the beijing cuihu wetland, china, using the 16s rdna library technique. in total, 184 individual sequences were used to assess the diversity of endophytic bacteria. phylogenetic analysis revealed that 161 clones (87.5%) were affiliated with proteobacteria, other clones grouped into cytophaga/flexibacter/bacteroids (3.3%), fusobacteria (3.8%), and nearly 5% were uncultured ... | 2010 | 21111814 |
| a meta-analysis of 16s rrna gene clone libraries from the polymicrobial black band disease of corals. | black band disease (bbd) is a polymicrobial disease affecting corals on reefs worldwide. since 2002, researchers have constructed clone libraries from the bbd consortium using 16s rrna gene primers targeting a variety of phyla. in the present study, a meta-analysis was conducted of published libraries from 2002 through the present that contain bacterial sequence data associated with individual clones and bbd samples. the libraries analyzed were from 87 bbd samples, collected from 16 species of s ... | 2010 | 21114503 |
| general suppression of escherichia coli o157:h7 in sand-based dairy livestock bedding. | sand bedding material is frequently used in dairy operations to reduce the occurrence of mastitis and enhance cow comfort. one objective of this work was to determine if sand-based bedding also supported the microbiologically based suppression of an introduced bacterial pathogen. bedding samples were collected in summer, fall, and winter from various locations within a dairy operation and tested for their ability to suppress introduced populations of escherichia coli o157:h7. all sources of bedd ... | 2011 | 21257815 |
| shifts in coastal antarctic marine microbial communities during and after melt water-related surface stratification. | antarctic coastal waters undergo major physical alterations during summer. increased temperatures induce sea-ice melting and glacial melt water input, leading to strong stratification of the upper water column. we investigated the composition of micro-eukaryotic and bacterial communities in ryder bay, antarctic peninsula, during and after summertime melt water stratification, applying community fingerprinting (denaturing gradient gel electrophoresis) and sequencing analysis of partial 18s and 16 ... | 2011 | 21303395 |
| genetic and functional diversities of bacterial communities in the rhizosphere of arachis hypogaea. | bioinoculants are environmentally friendly, energy efficient and economically viable resources in sustainable agriculture. knowledge of the structure and activities of microbial population in the rhizosphere of a plant is essential to formulate an effective bioinoculant. in this study, the bacterial community present in the rhizosphere of an important oilseed legume, arachis hypogaea (l.) was described with respect to adjoining bulk soil as a baseline control using a 16s rdna based metagenomic a ... | 2011 | 21380504 |
| bacterial community structure of a full-scale biofilter treating pig house exhaust air. | biological air filters represent a promising tool for treating emissions of ammonia and odor from pig facilities. quantitative fluorescence in situ hybridization (fish) and 16s rrna gene sequencing were used to investigate the bacterial community structure and diversity in a full-scale biofilter consisting of two consecutive compartments (front and back filter). the analysis revealed a highly specialized bacterial community of limited diversity, dominated by a few groups of betaproteobacteria (e ... | 2011 | 21514081 |
| diazotrophic microbial community of coastal microbial mats of the southern north sea. | the diazotrophic community in microbial mats growing along the shore of the north sea barrier island schiermonnikoog (the netherlands) was studied using microscopy, lipid biomarkers, stable carbon (δ(13) c(toc) ) and nitrogen (δ(15) n) isotopes as well as by constructing and analyzing 16s rrna gene libraries. depending on their position on the littoral gradient, two types of mats were identified, which showed distinct differences regarding the structure, development and composition of the microb ... | 2011 | 21535363 |
| bacterial populations and environmental factors controlling cellulose degradation in an acidic sphagnum peat. | northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. a large proportion of these peatlands consists of acidic sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. the degradation of cellulose, the major component of sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (ph 4.0) peat extracts. this process was almost ... | 2011 | 21564458 |
| [selective isolation and diversity of cold-adapted lipase-producing strains from permafrost soil at the terminus of a glacier in the tianshan mountains]. | the diversity of culturable lipase-producing bacterial strains from permafrost soils at the terminus of a glacier in the tianshan mountains was investigated. isolation and molecular phylogenetic analysis were performed to expand our knowledge on diversity of psychrotrophic and psychrophilic bacteria. in addition, efforts were made focusing on screening for cold active lipases. | 2011 | 21574385 |
| molecular diversity of bacteria in yunnan yellow cattle (bos taurs) from nujiang region, china. | the rumen content of four yunnan yellow cattle (bos taurs) were collected to determine the bacteria diversity by using 16s rrna gene sequence analysis. a total of 129 sequences were examined and the sequences were referred as 107 otu (operational taxonomy unit) according to the similarity level of 97% in gene sequence. similarity analysis revealed that yunnan yellow cattle had 12 sequences (10 otu) shared 97% or greater similarity with cultured rumen bacteria butyrivibrio fibrisolvens, succinicl ... | 2011 | 21598111 |
| isolation and phylogenetic classification of culturable psychrophilic prokaryotes from the collins glacier in the antarctica. | culturable psychrophilic prokaryotes were obtained of samples of glacier sediment, seaside mud, glacier melted ice, and deschampsia antarctica rhizosphere from collins glacier, antarctica. the taxonomic classification was done by a culture-dependent molecular approach involving the amplified ribosomal dna restriction analysis. two hundred sixty colonies were successfully isolated and sub-cultivated under laboratory conditions. the analysis showed a bacterial profile dominated by beta-proteobacte ... | 2011 | 21625878 |
| flavobacterium johnsoniae as model organism for characterizing biopolymer utilization in oligotrophic freshwater environments. | biopolymers are important substrates for heterotrophic bacteria in oligotrophic freshwater environments, but information on bacterial growth kinetics with biopolymers is scarce. the objective of this study was to characterize bacterial biopolymer utilization in these environments by assessing the growth kinetics of flavobacterium johnsoniae strain a3, which is specialized in utilizing biopolymers at µg l(-1) levels. growth of strain a3 with amylopectin, xyloglucan, gelatin, maltose, or fructose ... | 2011 | 21803894 |
| marine bacterioplankton diversity and community composition in an antarctic coastal environment. | the bacterial community inhabiting the water column at terra nova bay (ross sea, antarctica) was examined by the fluorescent in situ hybridization (fish) technique and the genotypic and phenotypic characterization of 606 bacterial isolates. overall, the fish analysis revealed a bacterioplankton composition that was typical of antarctic marine environments with the cytophaga/flavobacter (cf) group of bacteroidetes that was equally dominant with the actinobacteria and gammaproteobacteria. as sampl ... | 2011 | 21748267 |
| planktonic microbes in the gulf of maine area. | in the gulf of maine area (goma), as elsewhere in the ocean, the organisms of greatest numerical abundance are microbes. viruses in goma are largely cyanophages and bacteriophages, including podoviruses which lack tails. there is also evidence of mimivirus and chlorovirus in the metagenome. bacteria in goma comprise the dominant sar11 phylotype cluster, and other abundant phylotypes such as sar86-like cluster, sar116-like cluster, roseobacter, rhodospirillaceae, acidomicrobidae, flavobacteriales ... | 2011 | 21698243 |
| structured multiple endosymbiosis of bacteria and archaea in a ciliate from marine sulfidic sediments: a survival mechanism in low oxygen, sulfidic sediments? | marine micro-oxic to sulfidic environments are sites of intensive biogeochemical cycling and elemental sequestration, where prokaryotes are major driving forces mediating carbon, nitrogen, sulfur, phosphorus, and metal cycles, important from both biogeochemical and evolutionary perspectives. associations between single-celled eukaryotes and bacteria and/or archaea are common in such habitats. here we describe a ciliate common in the micro-oxic to anoxic, typically sulfidic, sediments of santa ba ... | 2011 | 21833311 |
| novel family of carbohydrate-binding modules revealed by the genome sequence of spirochaeta thermophila dsm 6192. | spirochaeta thermophila is a thermophilic, free-living, and cellulolytic anaerobe. the genome sequence data for this organism have revealed a high density of genes encoding enzymes from more than 30 glycoside hydrolase (gh) families and a noncellulosomal enzyme system for (hemi)cellulose degradation. functional screening of a fosmid library whose inserts were mapped on the s. thermophila genome sequence allowed the functional annotation of numerous gh open reading frames (orfs). seven different ... | 2011 | 21685171 |
| Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes. | To follow the anaerobic degradation of organic matter in tidal-flat sediments, a stimulation experiment with (13)C-labeled Spirulina biomass (130?mg per 21?g sediment slurry) was conducted over a period of 24 days. A combination of microcalorimetry to record process kinetics, chemical analyses of fermentation products and RNA-based stable-isotope probing (SIP) to follow community changes was applied. Different degradation phases could be identified by microcalorimetry: Within 2 days, heat output ... | 2011 | 21918576 |
| diel fluctuations in the abundance and community diversity of coastal bacterioplankton assemblages over a tidal cycle. | the diel change in abundance and community diversity of the bacterioplankton assemblages within the pacific ocean at a fixed location in monterey bay, california (usa) were examined with several culture-independent (i.e., nucleic acid staining, fluorescence in situ hybridization {fish}, and 16s ribosomal rna gene libraries) approaches over a tidal cycle. fish analyses revealed the quantitative predominance of bacterial members belonging to the cytophaga-flavobacterium cluster as well as two prot ... | 2011 | 21915631 |
| the use of warmed water treatment to induce protective immunity against the bacterial cold-water disease pathogen flavobacterium psychrophilum in ayu (plecoglossus altivelis). | we investigated the induction of protective immunity against bacterial cold-water disease (bcwd) caused by flavobacterium psychrophilum by warmed water treatment in ayu (plecoglossus altivelis). fish were immersed in a live bacterial suspension (10(7) cfu ml(-1)) for 30 min and placed in 700 l concrete tanks. the 28 °c warmed water treatment lasted 3 days and began 1, 6, and 24 h after immersion in the live bacterial suspension. a naïve control fish group was immersed in a sterilized modified cy ... | 2011 | 22209763 |
| identification of a denitrifying gliding bacterium, isolated from soil and able to reduce nitrous oxide in the presence of sulfide and acetylene, as flexibacter canadensis. | we have reexamined the properties of a gliding bacterium, is-11, which was previously isolated from soil because of its ability to denitrify and to reduce nitrous oxide in the presence of sulfide and normally inhibitory concentrations of acetylene. occurrence of such an organism may have important implications for the use of the acetylene inhibition assay for measuring denitrification rates in reduced, sulfidic environments. although originally tentatively identified as a cytophaga sp., extensiv ... | 1990 | 22049936 |
| biotreatment of o-nitrobenzaldehyde manufacturing wastewater and changes in activated sludge flocs in a sequencing batch reactor. | o-nitrobenzaldehyde manufacturing wastewater is characterized for being highly saline, with its tn content and dissolved organic concentrations giving rise to high cod loads. a sequencing batch reactor was established to investigate the effects of major processing variables, such as srt and hrt, on system performance. the optimal cod (86%) and tn (40.9%) removal efficiencies were obtained at 16d (srt) and 12h (hrt). design equations were developed by applying experimental data. changes in sludge ... | 2012 | 22130085 |
| bacterial communities in an ultrapure water containing storage tank of a power plant. | ultrapure waters (upws) containing low levels of organic and inorganic compounds provide extreme environment. on contrary to that microbes occur in such waters and form biofilms on surfaces, thus may induce corrosion processes in many industrial applications. in our study, refined saltless water (upw) produced for the boiler of a hungarian power plant was examined before and after storage (sampling the inlet [tke] and outlet [tku] waters of a storage tank) with cultivation and culture independen ... | 2011 | 22207294 |
| Development of replicative oriC plasmids and their versatile use in genetic manipulation of Cytophaga hutchinsonii. | Cytophaga hutchinsonii is a Gram-negative aerobic soil bacterium which can digest crystalline cellulose completely through a strategy different from that of the well-studied cellulolytic aerobic fungi and anaerobic bacteria. However, despite the availability of a published genome sequence, studies on this organism have been very limited because of the lack of a genetic manipulation system. This paper describes the development of replicative oriC plasmids, carrying the replication origin of the C ... | 2011 | 21935590 |
| the structural diversity of carbohydrate antigens of selected gram-negative marine bacteria. | marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. among these biologically active molecules, t ... | 2011 | 22073003 |
| Rapid successions affect microbial N-acetyl-glucosamine uptake patterns during a lacustrine spring phytoplankton bloom. | The vernal successions of phytoplankton, heterotrophic nanoflagellates (HNF) and viruses in temperate lakes result in alternating dominance of top-down and bottom-up factors on the bacterial community. This may lead to asynchronous blooms of bacteria with different life strategies and affect the channelling of particular components of the dissolved organic matter (DOM) through microbial food webs. We followed the dynamics of several bacterial populations and of other components of the microbial ... | 2011 | 22082109 |
| evidence for horizontal gene transfer from bacteroidetes bacteria to dinoflagellate minicircles. | dinoflagellate protists harbor a characteristic peridinin-containing plastid that evolved from a red or haptophyte alga. in contrast to typical plastids that have ∼100-200 kb circular genomes, the dinoflagellate plastid genome is composed of minicircles that each encode 0-5 genes. it is commonly assumed that dinoflagellate minicircles are derived from a standard plastid genome through drastic reduction and fragmentation. however, we demonstrate that the ycf16 and ycf24 genes (encoded on the cera ... | 2011 | 22075114 |
| patterns of marine bacterioplankton biodiversity in the surface waters of the scotia arc, southern ocean. | spatial patchiness in marine surface bacterioplankton populations was investigated in the southern ocean, where the antarctic circumpolar current meets the islands of the scotia arc and is subjected to terrestrial input, upwelling of nutrients and seasonal phytoplankton blooms. total bacterioplankton population density, group specific taxonomic distribution and six out of eight dominant members of the bacterioplankton community were found to be consistent across eighteen near shore sites at eigh ... | 2012 | 22273466 |