Actinorhodopsins (ActRs) are recently discovered proteorhodopsins present in Actinobacteria, enabling them to adapt to a wider spectrum of environmental conditions. Frequently, a large fraction of freshwater bacterioplankton belongs to the acI lineage of Actinobacteria and codes the LG1 type of ActRs. In this paper we studied the genotype variability of the LG1 ActRs. We have constructed two clone libraries originating from two environmentally different habitats located in Central Europe; the large alkaline lake Mondsee (Austria) and the small humic reservoir Jiřická (the Czech Republic). The 75 yielded clones were phylogenetically analyzed together with all ActR sequences currently available in public databases. Altogether 156 sequences were analyzed and 13 clusters of ActRs were distinguished. Newly obtained clones are distributed over all three LG1 subgroups--LG1-A, B and C. Eighty percent of the sequences belonged to the acI lineage (LG1-A ActR gene bearers) further divided into LG1-A1 and LG1-A2 subgroups. Interestingly, the two habitats markedly differed in genotype composition with no identical sequence found in both samples of clones. Moreover, Jiřická reservoir contained three so far not reported clusters, one of them LG1-C related, presenting thus completely new, so far undescribed, genotypes of Actinobacteria in freshwaters.

• MeSH
• Actinobacteria klasifikace   genetika   růst a vývoj   MeSH
• bakteriální proteiny klasifikace   genetika   MeSH
• DNA bakterií chemie   genetika   MeSH
• ekosystém * MeSH
• fylogeneze MeSH
• genetická variace MeSH
• hybridizace in situ fluorescenční MeSH
• molekulární sekvence - údaje MeSH
• multigenová rodina genetika   MeSH
• polymerázová řetězová reakce MeSH
• sekvenční analýza DNA MeSH
• sladká voda mikrobiologie   MeSH
• zeměpis MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Rakousko MeSH

• Publikační typ
• abstrakt z konference MeSH

Bacteria of the genus Limnohabitans, more precisely the R-BT lineage, have a prominent role in freshwater bacterioplankton communities due to their high rates of substrate uptake and growth, growth on algal-derived substrates and high mortality rates from bacterivory. Moreover, due to their generally larger mean cell volume, compared to typical bacterioplankton cells, they contribute over-proportionally to total bacterioplankton biomass. Here we present genetic, morphological and ecophysiological properties of 35 bacterial strains affiliated with the Limnohabitans genus newly isolated from 11 non-acidic European freshwater habitats. The low genetic diversity indicated by the previous studies using the ribosomal SSU gene highly contrasted with the surprisingly rich morphologies and different patterns in substrate utilization of isolated strains. Therefore, the intergenic spacer between 16S and 23S rRNA genes was successfully tested as a fine-scale marker to delineate individual lineages and even genotypes. For further studies, we propose the division of the Limnohabitans genus into five lineages (provisionally named as LimA, LimB, LimC, LimD and LimE) and also additional sublineages within the most diversified lineage LimC. Such a delineation is supported by the morphology of isolated strains which predetermine large differences in their ecology.

• MeSH
• Betaproteobacteria klasifikace   genetika   růst a vývoj   metabolismus   MeSH
• biomasa MeSH
• ekosystém * MeSH
• fylogeneze MeSH
• genetická variace * MeSH
• molekulární sekvence - údaje MeSH
• RNA ribozomální 16S genetika   MeSH
• sladká voda mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Two bacterial strains, II-B4(T) and II-D5(T), isolated from the meso-eutrophic freshwater Římov reservoir (Czech Republic), were characterized phenotypically, phylogenetically and chemotaxonomically. Both strains were chemo-organotrophic, facultatively anaerobic, non-motile rods, with identical DNA G+C contents of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and their major fatty acids were C(16 : 1)ω7c/C(16 : 1)ω6c, C(16 : 0), C(18 : 1)ω7c/C(18 : 1)ω6c and C(12 : 0). Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA gene sequences of the two strains possessed 99.1 % similarity; however, the level of DNA-DNA reassociation was only 26.7 %. The strains can also be discriminated from each other by several chemotaxonomic and biochemical traits. Phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent the first isolated members of a narrow phylogenetic cluster (the so-called R-BT065 cluster) formed by a large number of environmental sequences and abundant populations detected in the pelagic zones of various freshwater habitats. We propose to place the two strains in separate novel species within the genus Limnohabitans, Limnohabitans planktonicus sp. nov., with the type strain II-D5(T) (=DSM 21594(T) =CIP 109844(T)), and Limnohabitans parvus sp. nov., with the type strain II-B4(T) (=DSM 21592(T) =CIP 109845(T)). The description of the genus Limnohabitans is emended accordingly.

• MeSH
• Comamonadaceae klasifikace   genetika   izolace a purifikace   MeSH
• DNA bakterií genetika   MeSH
• fenotyp MeSH
• fosfolipidy krev   MeSH
• fylogeneze * MeSH
• mastné kyseliny chemie   MeSH
• molekulární sekvence - údaje MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• sladká voda mikrobiologie   MeSH
• techniky typizace bakterií MeSH
• ubichinon chemie   MeSH
• zastoupení bazí MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization) probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S-23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus) patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of these bacteria. Instead, our observations suggest that the genus Limnohabitans, as well as its R-BT subgroup, represent ecologically heterogeneous taxa, which underwent pronounced ecological diversification.

• MeSH
• bakteriální RNA genetika   MeSH
• biodiverzita * MeSH
• Comamonadaceae fyziologie   MeSH
• fyziologická adaptace fyziologie   MeSH
• hybridizace in situ fluorescenční MeSH
• koncentrace vodíkových iontů MeSH
• mikrobiologie vody * MeSH
• RNA ribozomální 16S genetika   MeSH
• sladká voda mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

We studied the diversity of Limnohabitans using reverse line blot hybridization with Limnohabitans lineage-specific probes in the freshwater canyon-shaped Římov reservoir (Czech Republic). To examine the succession of distinct lineages, we performed (i) a study of an intensive spring sampling program at the lacustrine part of the Římov reservoir (from ice melt through a phytoplankton peak to the clear-water phase), and (ii) a seasonal study (April to November) when the occurrence of distinct Limnohabitans lineages was related to the inherent longitudinal heterogeneity of the reservoir. Significant spatiotemporal changes in the compositions of distinct Limnohabitans lineages allowed for the identification of "generalists" that were always present throughout the whole season as well as "specialists" that appeared in the reservoir only for limited periods of time or irregularly. Our results indicate that some phytoplankton groups, such as cryptophytes or cyanobacteria, and zooplankton composition were the major factors modulating the distribution and dynamics of distinct Limnohabitans lineages. The highest Limnohabitans diversity was observed during the spring algal bloom, whereas the lowest was during the summer cyanobacterial bloom. The microdiversity also markedly increased upstream in the reservoir, being highest at the inflow, and thus likely reflecting strong influences of the watershed.IMPORTANCE The genus Limnohabitans is a typical freshwater bacterioplankton and is believed to play a significant role in inland freshwater habitats. This work is unique in detecting and tracing different closely related lineages of this bacterial genus in its natural conditions using the semiquantitative reverse line blot hybridization method and in discovering the factors influencing the microdiversity, subtype alternations, and seasonality.

• MeSH
• Comamonadaceae klasifikace   genetika   izolace a purifikace   MeSH
• Cryptophyta růst a vývoj   MeSH
• ekosystém MeSH
• eutrofizace MeSH
• fytoplankton růst a vývoj   MeSH
• roční období MeSH
• sinice růst a vývoj   MeSH
• sladká voda mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH

Ramanovu spektroskopii lze v chemii použít nejen k určování chemického složení, ale také pro získávání dalších informací o struktuře materiálu. Ve spektrech semikrystalických polymerů lze nalézt vzájemně odlišné pásy charakteristické pro krystalickou nebo amorfní fázi, stanovit z nich krystalinitu a z ní odhadnout míru degradace polymeru. V předložené studii byly vyhodnoceny změny raménka pásu na vlnočtu 1733 cm−1 v Ramanových spektrech vlákna z poly(p-dioxanonu) podrobeného hydrolytické degradaci. Pro různě dlouhé doby degradace byly vypočteny obsahy ploch pod raménkem tohoto pásu a též byl proveden jeho modelový rozklad na předpokládané píky krystalické a amorfní fáze. Obsahy ploch pod raménkem i parametry modelových píků byly porovnány s hodnotami krystalinity získanými pomocí diferenční skenovací kalorimetrie, přičemž bylo dosaženo dobré shody. Tato práce ukazuje příklad využití Ramanovy spektroskopie při studiu hydrolytické degradace polymerů.

Raman spectroscopy can be used in chemistry not just to determine chemical composition, but also to obtain further information on the material structure. In the spectra of semi-crystalline polymers, distinct bands characteristic of the crystalline or the amorphous phase can be found, the degree of crystallinity determined from them, and the degree of polymer degradation estimated from the crystallinity. In the present study, changes in the 1733 cm−1 band shoulder in Raman spectra of poly(p-di­oxanone) fibres subjected to hydrolytic degradation were evaluated. For different degradation periods, the areas under the shoulder of this band were calculated and a model deconvolution of this band into assumed crystalline and amorphous peaks was also performed. The areas under the shoulder, as well as the model peaks' parameters, were compared with the crystallinity values obtained by differential scanning calorimetry, achieving a good agreement. This work shows an example of using Raman spectroscopy when studying the hydrolytic degradation of polymers.

• MeSH
• lidé MeSH
• polydioxanon chemie   MeSH
• polymery chemie   MeSH
• Ramanova spektroskopie * metody   MeSH
• Check Tag
• lidé MeSH

The distribution of the phylogenetically narrow R-BT065 cluster (Betaproteobacteria) in 102 freshwater lakes, reservoirs, and various ponds located in central Europe (a total of 122 samples) was examined by using a cluster-specific fluorescence in situ hybridization probe. These habitats differ markedly in pH, conductivity, trophic status, surface area, altitude, bedrock type, and other limnological characteristics. Despite the broad ecological diversity of the habitats investigated, the cluster was detected in 96.7% of the systems, and its occurrence was not restricted to a certain habitat type. However, the relative proportions of the cluster in the total bacterioplankton were significantly lower in humic and acidified lakes than in pH-neutral or alkaline habitats. On average, the cluster accounted for 9.4% of the total bacterioplankton (range, 0 to 29%). The relative abundance and absolute abundance of these bacteria were significantly and positively related to higher pH, conductivity, and the proportion of low-molecular-weight compounds in dissolved organic carbon (DOC) and negatively related to the total DOC and dissolved aromatic carbon contents. Together, these parameters explained 55.3% of the variability in the occurrence of the cluster. Surprisingly, no clear relationship of the R-BT065 bacteria to factors indicating the trophic status of habitats (i.e., different forms of phosphorus and chlorophyll a content) was found. Based on our results and previously published data, we concluded that the R-BT065 cluster represents a ubiquitous, highly active segment of bacterioplankton in nonacidic lakes and ponds and that alga-derived substrates likely form the main pool of substrates responsible for its high growth potential and broad distribution in freshwater habitats.

• MeSH
• Betaproteobacteria klasifikace   genetika   izolace a purifikace   MeSH
• chlorofyl analýza   MeSH
• DNA bakterií chemie   MeSH
• ekosystém MeSH
• Eukaryota genetika   MeSH
• fosfor analýza   MeSH
• fylogeneze MeSH
• genetická variace MeSH
• hybridizace in situ fluorescenční MeSH
• mikrobiologie vody MeSH
• nadmořská výška MeSH
• počet mikrobiálních kolonií MeSH
• ribozomální DNA genetika   MeSH
• RNA ribozomální 16S genetika   MeSH
• RNA ribozomální 18S genetika   MeSH
• sekvenční analýza DNA MeSH
• shluková analýza MeSH
• skleníkový efekt MeSH
• sladká voda chemie   mikrobiologie   MeSH
• uhlík analýza   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa MeSH

Different bacterial strains can have different value as food for heterotrophic nanoflagellates (HNF), thus modulating HNF growth and community composition. We examined the influence of prey food quality using four Limnohabitans strains, one Polynucleobacter strain and one freshwater actinobacterial strain on growth (growth rate, length of lag phase and growth efficiency) and community composition of a natural HNF community from a freshwater reservoir. Pyrosequencing of eukaryotic small subunit rRNA amplicons was used to assess time-course changes in HNF community composition. All four Limnohabitans strains and the Polynucleobacter strain yielded significant HNF community growth while the actinobacterial strain did not although it was detected in HNF food vacuoles. Notably, even within the Limnohabitans strains we found significant prey-related differences in HNF growth parameters, which could not be related only to size of the bacterial prey. Sequence data characterizing the HNF communities showed also that different bacterial prey items induced highly significant differences in community composition of flagellates. Generally, Stramenopiles dominated the communities and phylotypes closely related to Pedospumella (Chrysophyceae) were most abundant bacterivorous flagellates rapidly reacting to addition of the bacterial prey of high food quality.

• MeSH
• Actinobacteria fyziologie   MeSH
• Burkholderiaceae fyziologie   MeSH
• časové faktory MeSH
• Comamonadaceae fyziologie   MeSH
• Eukaryota růst a vývoj   metabolismus   fyziologie   MeSH
• fyziologie bakterií MeSH
• geny rRNA genetika   MeSH
• heterotrofní procesy MeSH
• potravní řetězec MeSH
• sladká voda mikrobiologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• filozofie MeSH
• literatura MeSH
• umění MeSH
• Publikační typ
• periodika MeSH

• Konspekt
• Umění
• NLK Obory
• humanitní vědy a umění