Publications

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
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
characterization of bacterial diversity in two aerated lagoons of a wastewater treatment plant using pcr-dgge analysis.	aerated lagoons are commonly used for domestic and industrial wastewater treatment due to their low cost and minimal need of operational requirements. however, little information is known regarding microbial communities that inhabit these ecosystems. in this study, a 16s-dgge approach was used to estimate bacterial diversity and to monitor community changes in two aerated lagoons from a wastewater treatment plant receiving urban and industrial effluents. pronounced shifts between bacterial commu ...	2009	17681740
vertical distribution and phylogenetic composition of bacteria in the eastern tropical north pacific ocean.	the vertical community structure of bacteria along a depth profile in the eastern tropical north pacific ocean (13 degrees n, 104 degrees w) was studied by flow cytometry measurement and 16s rrna gene clone libraries analysis. picoeukaryotes and synechococcus peaked at 30 m and decreased sharply below 50 m, while prochlorococcus peaked at both 30 and 100 m layers and disappeared below 200 m. heterotrophic bacteria peaked above shallow thermocline and decreased along the depth profile. sequences ...	2009	18387795
quantitative population dynamics of microbial communities in plankton-fed microbial fuel cells.	this study examines changes in diversity and abundance of bacteria recovered from the anodes of microbial fuel cells (mfcs) in relation to anode potential, power production and geochemistry. mfcs were batch-fed with plankton, and two systems were maintained at different potentials whereas one was at open circuit for 56.8 days. bacterial phylogenetic diversity during peak power was assessed from 16s rdna clone libraries. throughout the experiment, microbial community structure was examined using ...	2009	19242533
ingestion of bacteria overproducing dnak attenuates vibrio infection of artemia franciscana larvae.	feeding of bacterially encapsulated heat shock proteins (hsps) to invertebrates is a novel way to limit vibrio infection. as an example, ingestion of escherichia coli overproducing prokaryotic hsps significantly improves survival of gnotobiotically cultured artemia larvae upon challenge with pathogenic vibrio campbellii. the relationship between hsp accumulation and enhanced resistance to infection may involve dnak, the prokaryotic equivalent to hsp70, a major molecular chaperone in eukaryotic c ...	2009	19373565
[morphologic changes in the life cycle of cytophaga hutchinsonii].	to study the morphological changes of cytophaga hutchinsonii cell during its life circle.	2009	19388259
[bacterial diversity of disused thermal vents in tibetan yangbajing region].	to study the bacterial diversity in sediment and water from two disused thermal vents in yangbajing, tibet, china.	2009	19445178
[bacterial diversity in guangxi buffalo rumen].	to analyze the diversity of bacterial community in guangxi buffalo rumen and to identify the possible cellulolytic bacterial group.	2009	19445183
effects of seawater ozonation on biofilm development in aquaculture tanks.	microbial biofilms developing in aquaculture tanks represent a reservoir for opportunistic bacterial pathogens, and procedures to control formation and bacterial composition of biofilms are important for the development of commercially viable aquaculture industries. this study investigated the effects of seawater ozonation on biofilm development on microscope glass slides placed in small-scale aquaculture tanks containing the live feed organism artemia. fluorescence in situ hybridization (fish) ...	2009	19446976
inorganic phosphorus and nitrogen modify composition and diversity of microbial communities in water of mesotrophic lake.	the effects of inorganic nutrients (n, p) enrichment of mesotrophic lake water on changes in bacterial and protistan (heterotrophic nanoflagellates and ciliates) communities compositions were studied in the mesocosm experiment. phosphorus (po4(3-)) and nitrogen (nh4+) alone and in combination were added to three types of experimental mesocosms. mesocosms results suggested that simultaneous addition of p and n stimulated phytoplankton growth and production rates of bacterial biomass its turnover ...	2009	19469290
extremophile culture collection from andean lakes: extreme pristine environments that host a wide diversity of microorganisms with tolerance to uv radiation.	a total of 88 bacterial strains were isolated from six andean lakes situated at altitudes ranging from 3,400 to 4,600 m above sea level: l. aparejos (4,200 m), l. negra (4,400 m), l. verde (4,460 m), l. azul (4,400 m), l. vilama (4,600 m), and salina grande (3,400 m). salinity ranged from 0.4 to 117 ppm. general diversity was determined by denaturing gradient gel electrophoresis (dgge) analysis. from the excised dgge bands, 182 bacterial sequences of good quality were obtained. gammaproteobacter ...	2009	19495855
microbial diversity of a sulfide black smoker in main endeavour hydrothermal vent field, juan de fuca ridge.	submarine hydrothermal vents are among the least-understood habitats on earth but have been the intense focus of research in the past 30 years. an active hydrothermal sulfide chimney collected from the dudley site in the main endeavour vent field (mef) of juan de fuca ridge was investigated using mineralogical and molecular approaches. mineral analysis indicated that the chimney was composed mainly of fe-, zn-and cu-rich sulfides. according to phylogenetic analysis, within the crenarchaeota, clo ...	2009	19557339
a small population of planktonic flavobacteria with disproportionally high growth during the spring phytoplankton bloom in a prealpine lake.	bacterioplankton growth in temperate lake zurich (switzerland) was studied during the spring phytoplankton bloom by in situ techniques and short-term dilution bioassays. a peak of chlorophyll a (chl a) concentrations was followed by a rise of bacterial cell numbers and leucine assimilation rates, of the proportions of cells incorporating 5-bromo-2-deoxyuridine (brdu), and of community net growth rates in dilution cultures. incorporation of brdu was low in betaproteobacteria (2 +/- 1%), indicatin ...	2009	19601962
marinifilum fragile gen. nov., sp. nov., isolated from tidal flat sediment.	a facultatively anaerobic, moderately halophilic, gram-negative, filamentous bacterium, designated jc2469t, was isolated from tidal flat sediment in korea. phylogenetic analysis based on 16s rrna gene sequences showed that the isolate belonged to the phylum bacteroidetes and its closest taxonomic relative was cytophaga fermentans ncimb 2218t (89.6% sequence similarity). cells appeared as filaments during exponential growth, but became fragmented to rods at stationary phase. spherical cells were ...	2009	19620374
characterization of the bacterial community associated with body wall lesions of tripneustes gratilla (echinoidea) using culture-independent methods.	the bacterial community associated with skin lesions of the sea urchin tripneustes gratilla was investigated using 16s ribosomal rna gene cloning and fluorescent in situ hybridization (fish). all clones were classified in the alphaproteobacteria, gammaproteobacteria and cytophaga-flexibacter-bacteroides (cfb) bacteria. most of the alphaproteobacteria were related to the roseobacter lineage and to bacteria implicated in marine diseases. the majority of the gammaproteobacteria were identified as v ...	2009	19041326
microbial community variation and functions to excess sludge reduction in a novel gravel contact oxidation reactor.	excess biomass produced within the degradation processes of organic pollutants is creating environmental challenges. the gravel contact oxidation reactor (gcor) filled with crushed stone globular aggregates as carriers, has been demonstrated capable of reducing the excess sludge effectively in some pilot and small-scale engineering studies. in order to evaluate the variation and structure of the microbial community and their functions to excess sludge reduction in gcor, a conventional activated ...	2009	19070427
isolation and identification of bacteriophages infecting ayu plecoglossus altivelis altivelis specific flavobacterium psychrophilum.	in order to investigate methods for controlling systemic bacterial coldwater disease (cwd), bacteriophages that infect flavobacterium psychrophilum were isolated by the enrichment method from pond water collected from japanese ayu farms. the five phages isolated were classified as members of myoviridae (pfpw-3, pfpc-y), podoviridae (pfpw-6, pfpw-7), and siphoviridae (pfpw-8) and had highly variable patterns of infectivity for different f. psychrophilum isolates (n=128). the stability tests of th ...	2010	19647377
bacterial diversity in the rumen of gayals (bos frontalis), swamp buffaloes (bubalus bubalis) and holstein cow as revealed by cloned 16s rrna gene sequences.	libraries of rumen bacterial 16s rrna gene sequences of gayals (bos frontalis) and swamp buffaloes (bubalus bubalis) were cloned and sequenced in the present work to compare the bacterial diversity with the third published library of holstein cow. sequence similarity of 97% was used as the definition of operational taxonomic unit (otu). the majority of the 470 sequences retrieved fell into the phyla of low g + c subdivision (329 sequences) and cytophaga-flexibacter-bacteroides (cfb, 123 sequence ...	2010	19662514
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
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
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
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
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
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
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
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
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
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
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
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