polynucleobacter necessarius, an obligate bacterial endosymbiont of the hypotrichous ciliate euplotes aediculatus, is a member of the beta-subclass of almost full length 16s rrna gene of the obligate bacterial endosymbiont polynucleobacter necessarius was amplified using the polymerase chain reaction in combination with site-specific primers. the amplified dna was directly sequenced and compared with other bacterial 16s rrna sequences. p. necessarius belongs to the beta-subclass of proteobacteria and shows the closest relationship to alcaligenes eutrophus, burkholderia solanacearum, and b. pickettii. in proteobacteria and shows the closest ...19968595875
isolation of strains belonging to the cosmopolitan polynucleobacter necessarius cluster from freshwater habitats located in three climatic zones.more than 40 bacterial strains belonging to the cosmopolitan polynucleobacter necessarius cluster (betaproteobacteria) were isolated from a broad spectrum of freshwater habitats located in three climatic zones. sequences affiliated with the freshwater p. necessarius cluster are among the most frequently detected in studies on bacterial diversity in freshwater ecosystems. despite this frequent detection with culture-independent techniques and the cosmopolitan occurrence of members affiliated with ...200312957910
members of a readily enriched beta-proteobacterial clade are common in surface waters of a humic lake.humic lakes are systems often characterized by irregular high input of dissolved organic carbon (doc) from the catchment. we hypothesized that specific bacterial groups which rapidly respond to changes in doc availability might form large populations in such habitats. seasonal changes of microbial community composition were studied in two compartments of an artificially divided bog lake with contrasting doc inputs. these changes were compared to community shifts induced during short-term enrichm ...200314602613
bacterial endocytobionts of ciliophora and their interactions with the host cell.ciliates may be hosts for numerous bacteria, which can occupy almost all cellular compartments of the protists. about 200 ciliate species are recorded as hosts of different intracellular bacteria, being a small part of the diversity for such types of endocytobiosis in nature. in the paramecium genus alone close to 60 types of bacteria adapted for intracellular life are known. in this review extensive material concerning the variety of endocytobionts, their categories, and their interaction with ...200415261739
strain-specific differences in the grazing sensitivities of closely related ultramicrobacteria affiliated with the polynucleobacter cluster.ultramicrobacteria (cell volume < 0.1 microm(3)) are the numerically dominant organisms in the plankton of marine and freshwater habitats. flagellates and other protists are assumed to be the most important predators of these ultramicrobacteria as well as of larger planktonic bacteria. however, due to controversial observations conducted previously, it is not clear as to whether fractions of the ultramicrobacteria are resistant to flagellate predation. furthermore, it is not known if closely rel ...200415466515
polynucleobacter bacteria in the brackish-water species euplotes harpa (ciliata hypotrichia).we have found a polynucleobacter bacterium in the cytoplasm of euplotes harpa, a species living in a brackish-water habitat, with a cirral pattern not corresponding to that of the freshwater euplotes species known to harbor this type of bacteria. the symbiont has been found in three strains of the species, obtained by clonal cultures from ciliates collected in different geographic regions. the 16s rrna gene sequence of this bacterium identifies it as a member of the beta-proteobacterial genus po ...200515817116
low intraspecific diversity in a polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond.cultivation-dependent and -independent methods were combined to investigate the microdiversity of a polynucleobacter subcluster population (betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. fluorescent in situ hybridization with two probes specific for the narrow subcluster c (pnecc bacteria) of the pol ...200516085847
bacterial diversity of metagenomic and pcr libraries from the delaware determine whether metagenomic libraries sample adequately the dominant bacteria in aquatic environments, we examined the phylogenetic make-up of a large insert metagenomic library constructed with bacterial dna from the delaware river, a polymerase chain reaction (pcr) library of 16s rrna genes, and community structure determined by fluorescence in situ hybridization (fish). the composition of the libraries and community structure determined by fish differed for the major bacterial groups in ...200516309387
differences in structure and dynamics of polynucleobacter communities in a temperate and a subtropical lake, revealed at three phylogenetic levels.the results of ecological studies investigating bacteria by cultivation-independent methods are expected to be influenced by the phylogenetic resolution of the applied molecular tools. this potential influence was investigated in a comparative community study on polynucleobacter cluster bacteria (betaproteobacteria) inhabiting the pelagic of the large, shallow, partially hypertrophic taihu lake located in subtropical east asia, and the deep oligo-mesotrophic lake mondsee located in temperate cen ...200616819951
bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the tibetan plateau, china.the influence of altitude and salinity on bacterioplankton community composition (bcc) in 16 high-mountain lakes located at altitudes of 2,817 to 5,134 m on the eastern qinghai-xizang (tibetan) plateau, china, spanning a salinity gradient from 0.02% (freshwater) to 22.3% (hypersaline), was investigated. three different methods, fluorescent in situ hybridization, denaturing gradient gel electrophoresis (dgge) with subsequent band sequencing, and reverse line blot hybridization (rlb) with probes t ...200616885301
high predictability of the seasonal dynamics of a species-like polynucleobacter population in a freshwater of the key questions in microbial ecology is if seasonal patterns of bacterial community composition (bcc) observed in one year repeat in the following years. we have investigated if the recorded annual dynamics of a species-like polynucleobacter (subcluster pnecb) population allowed the prediction of the population dynamics in another year. the abundance of pnecb bacteria in the pelagic of temperate lake mondsee was investigated by fluorescence in situ hybridization (fish) over three consec ...200616913925
endosymbiosis in statu nascendi: close phylogenetic relationship between obligately endosymbiotic and obligately free-living polynucleobacter strains (betaproteobacteria).bacterial strains affiliated to the phylogenetically shallow subcluster c (pnecc) of the polynucleobacter cluster, which is characterized by a minimal 16s rrna gene sequence similarity of approximately 98.5%, have been reported to occur as obligate endosymbionts of ciliates (euplotes spp.), as well as to occur as free-living cells in the pelagic zone of freshwater habitats. we investigated if these two groups of closely related bacteria represent strains fundamentally differing in lifestyle, or ...200717222133
grazer and virus-induced mortality of bacterioplankton accelerates development of flectobacillus populations in a freshwater community.we present a detailed analysis of the effects of distinct bacterial mortality factors, viral lysis and heterotrophic nanoflagellates (hnf) bacterivory, associated with the development of filamentous flectobacillus populations. reservoir bacterioplankton communities were subjected to additions of both hnf and viruses together, or hnf alone, and then incubated in situ in dialyses bags. for distinct bacterial groups, mortality or growth stimulation was analysed by examining bacterial prey ingested ...200717298377
top-down and bottom-up induced shifts in bacterial abundance, production and community composition in an experimentally divided humic lake.we examined in situ abundance and activities of the major bacterial groups in the two most distinct compartments of experimentally divided lake grosse fuchskuhle (germany). the selected south-west (sw) and north-east basin (ne) differ substantially in their major chemical and biological parameters that potentially influence the dynamics and composition of microbial communities. water from the basins were incubated in dialysis bags, which allowed for a relatively free exchange of nutrients, limit ...200818190513
ecophysiological differences of betaproteobacterial populations in two hydrochemically distinct compartments of a subtropical lagoon.we studied the population sizes and substrate incorporation patterns of three phylogenetic groups of betaproteobacteria in a coastal subtropical lagoon that is characterized by a sharp transition from humic freshwater to turbid brackish water. various cellular processes were addressed by short-term incubations with four radiolabelled compounds and microautoradiographic assessment of substrate incorporation. group-specific differences in the abundances and the respective physiological state of th ...200919040452
effective isolation of bacterioplankton genus polynucleobacter from freshwater environments grown on photochemically degraded dissolved organic matter.effective isolation of freshwater bacterioplankton belonging to genus polynucleobacter from a shallow eutrophic lake and its tributary was achieved by size-selective filtration with a 0.7-mum pore filter and cultivation on r2a agar medium. partial 16s rrna gene analysis showed that over 80% of all the strains were highly similar to the polynucleobacter cluster. essential medium components for effective cultivation are pyruvate, yeast extract and peptone, whereas soluble starch and glucose are no ...200919049496
substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake.bacterial incorporation of glucose, leucine, acetate and 4-hydroxybenzoic acid (hba) was investigated in an artificially divided humic lake (grosse fuchskuhle, germany). two basins with contrasting influx of allochthonous organic carbon were sampled during late summer stratification (oxic and anoxic layers) and after autumn mixing. high total and cell-specific incorporation rates were observed for glucose and hba in stratified and mixed waters respectively, but only a small fraction of bacteria ...200919320716
isolation and characterization of low nucleic acid (lna)-content bacteria.most planktonic bacteria are 'uncultivable' with conventional methods. flow cytometry (fcm) is one approach that has been taken to study these bacteria. in natural aquatic environments, bacteria with high nucleic acid (hna) and low nucleic acid (lna) content are commonly observed with fcm after staining with fluorescent dyes. although several studies have focused on the relative abundance and in situ activities of these two groups, knowledge on the growth of particularly lna bacteria is largely ...200919421234
involvement of cell surface structures in size-independent grazing resistance of freshwater actinobacteria.we compared the influences of grazing by the bacterivorous nanoflagellate poterioochromonas sp. strain ds on ultramicrobacterial actinobacteria affiliated with the luna-2 cluster and ultramicrobacterial betaproteobacteria of the species polynucleobacter cosmopolitanus. these bacteria were almost identical in size (<0.1 microm(3)) and shape. predation on a polynucleobacter strain resulted in a reduction of >86% relative to the initial bacterial cell numbers within 20 days, while in comparable pre ...200919502450
emended description of the genus polynucleobacter and the species polynucleobacter necessarius and proposal of two subspecies, p. necessarius subsp. necessarius subsp. nov. and p. necessarius subsp. asymbioticus subsp. nov.heckmann and schmidt described the genus polynucleobacter for bacterial endosymbionts of freshwater ciliates affiliated with the genus euplotes, and the species polynucleobacter necessarius for obligate endosymbionts living in the cytoplasm of euplotes aediculatus. pure cultures of the type strain could not be established due to the obligate nature of the symbiotic relationship between the endosymbionts and their hosts. therefore, polynucleobacter necessarius is one of a few bacterial species wi ...200919567561
polynucleobacter cosmopolitanus sp. nov., free-living planktonic bacteria inhabiting freshwater lakes and rivers.five heterotrophic, aerobic, catalase- and oxidase-positive, non-motile strains were characterized from freshwater habitats located in austria, france, uganda, p. r. china and new zealand. the strains shared 16s rrna gene similarities of >/=99.3 %. the novel strains grew on nsy medium over a temperature range of 10-35 degrees c (two strains also grew at 5 degrees c and one strain grew at 38 degrees c) and a nacl tolerance range of 0.0-0.3 % (four strains grew up to 0.5 % nacl). the predominant f ...201019648339
ubiquity of polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogeneous 2000 km area.we present a survey on the distribution and habitat range of polynucleobacter necessarius ssp. asymbioticus (pnecc), a numerically and functionally important taxon in the plankton of freshwater systems. we systematically sampled stagnant freshwater habitats in a heterogeneous 2000 km(2) area, together with ecologically different habitats outside this area. in total, 137 lakes, ponds and puddles were investigated, which represent an enormous diversity of habitats differing, e.g. in depth (< 10 cm ...201020041938
changes in pelagic bacteria communities due to leaf litter many limnetic systems, the input of allochthonous organic matter, e.g., leaf litter, is a substantial source of dissolved organic carbon (doc) for pelagic bacteria, especially in fall and winter when autochthonous doc production is low. however, relatively little is known about community changes of pelagic lake bacteria due to leaf litter input which includes both the release of leaf leachates and microorganisms from the leaf litter into the surrounding water. therefore, we have experimentall ...201020198369
polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria.the heterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain mwh-poolgreena3(t), isolated from a rock pool filled with freshwater, was characterized. the strain grew on nsy medium over a nacl range of 0.0-0.3 % (w/v). whole-cell fatty acids were dominated by c(16 : 1)ω7c (feature 3), c(18 : 1)ω7c and straight-chain c(16 : 0); furthermore, the components c(12 : 0) and c(14 : 0) 2-oh were present. the dna g+c content was 48.3 mol%. phylogenetic analysis as ...201120435747
polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake.the heterotrophic, aerobic, facultatively anaerobic under denitrifying conditions, catalase- and oxidase-positive, non-motile strain mt-cbb6a5(t), which was isolated from an acidic lake located in wisconsin (usa), was characterized. the strain grew on nsy medium over a temperature range of 15-30 °c and a nacl range of 0.0-0.3 % (w/v). the predominant fatty acids were c(16 : 0), c(18 : 1)ω7c, 11-methyl c(18 : 1)ω7c, feature 3 (including c(16 : 1)ω7c), and feature 2 (including c(14 : 0) 3-oh). the ...201120435748
singlet oxygen, a neglected but important environmental factor: short-term and long-term effects on bacterioplankton composition in a humic lake.photolysis of dissolved organic matter (dom) leads to contrasting effects on bacterioplankton dynamics, i.e. stimulation and inhibition of bacterial activity. in particular, the role of short-lived reactive oxygen species (ros), e.g. singlet oxygen (¹o₂), in altering microbial activity and species composition has scarcely been investigated. therefore, we have artificially increased the natural rate of ¹o₂ formation in short-term (∼4 h) in situ and long-term (72 h) laboratory incubations of surfa ...201020636377
temporal patterns in glycolate-utilizing bacterial community composition correlate with phytoplankton population dynamics in humic lakes.previous observations of correlated community dynamics between phytoplankton and bacteria in lakes indicate that phytoplankton populations may influence bacterial community structure. to investigate the possibility that bacterial use of phytoplankton exudates contributes to observed patterns of community change, we characterized the diversity and dynamics of heterotrophic bacterioplankton with genetic potential to use glycolate, a photorespiration-specific exudate, in five lakes over a 15-week p ...201020652236
ubiquity of polynucleobacter necessarius subspecies asymbioticus results from ecological diversification.the subspecies polynucleobacter necessarius asymbioticus (> 99% 16s rrna similarity) has a cosmopolitan distribution and a ubiquitous occurrence in lentic freshwater habitats. we tested if the observed ubiquity of these free-living planktonic freshwater bacteria results from a euryoecious (generalist) adaptation of p. n. asymbioticus strains, or from ecological diversification within the subspecies. we developed a reverse line blot hybridization assay enabling the cultivation-independent detecti ...201121208356
polynucleobacter difficilis sp. nov., a planktonic freshwater bacterium affiliated with subcluster b1 of the genus polynucleobacter.strain am-8b5(t) isolated from lake sevan in armenia was phenotypically, chemotaxonomically, and phylogenetically characterized. this chemoorganoheterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain grew on nsy medium over a nacl range of 0.0-0.2 % (w/v), and a temperature range of 4-30 °c. whole-cell fatty acids were dominated by summed feature 3 (including c(16:1)?7c and iso-c(15:0)-2oh), c(16:0) and c(18:1)?7c. the components c(12:0)-2oh and c(16:1 ...201121441373
high-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (rbs) and aerobic anoxygenic phototrophs (aaps)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. however, their abundance and taxonomic identities remain largely unknown. we used a combination of single-cell and metagenomic dna sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwa ...201121716306
comparison of bacterial communities in the solimões and negro river tributaries of the amazon river based on small subunit rrna gene sequences.the microbiota of the amazon river basin has been little studied. we compared the structure of bacterial communities of the solimões and negro rivers, the main amazon river tributaries, based on analysis of 16s rrna gene sequences. water was sampled with a 3-l van dorn collection bottle; samples were collected at nine different points/depths totaling 27 l of water from each river. total dna was extracted from biomass retained by a 0.22-μm filter after sequential filtration of the water th ...201122183948
metagenomics of the water column in the pristine upper course of the amazon river.river water is a small percentage of the total freshwater on earth but represents an essential resource for mankind. microbes in rivers perform essential ecosystem roles including the mineralization of significant quantities of organic matter originating from terrestrial habitats. the amazon river in particular is famous for its size and importance in the mobilization of both water and carbon out of its enormous basin. here we present the first metagenomic study on the microbiota of this river. ...201121915244
alga-derived substrates select for distinct betaproteobacterial lineages and contribute to niche separation in limnohabitans strains.we examined the proportions of major betaproteobacteria subgroups within bacterial communities in diverse nonaxenic, monospecific cultures of algae or cyanobacteria: four species of cryptophyta (genera cryptomonas and rhodomonas), four species of chlorophyta (genera pediastrum, staurastrum, and chlamydomonas), and two species of cyanobacteria (genera dolichospermum and aphanizomenon). in the cryptophyta cultures, betaproteobacteria represented 48 to 71% of total bacteria, the genus limnohabitans ...201121873481
Dissolved Organic Carbon as Major Environmental Factor Affecting Bacterioplankton Communities in Mountain Lakes of Eastern Japan.Relationships between environmental factors and bacterial communities were investigated in 41 freshwater lakes located in mountainous regions of eastern Japan. Bacterioplankton community composition (BCC) was determined by polymerase chain reaction-denaturing gradient gel electrophoresis of the 16S rRNA gene and then evaluated on the basis of physicochemical and biological variables of the lakes. Canonical correspondence analysis revealed that BCC of oligotrophic lakes was significantly influenc ...201122109097
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 ...201122207294
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