Comparison of RNA- and DNA-based species diversity investigations in rhizoplane bacteriology with respect to chloroplast sequence exclusion

Dispersal timing and drought history influence the response of bacterioplankton to drying-rewetting stress

The extent and frequency of drought episodes is expected to increase in the following decades making it a crucial stress factor for smaller water bodies. However, very little is known about how bacterioplankton is affected by increased evaporation and how these communities reassemble after rewetting. Here, we present results from a microcosm experiment that assessed the effect of drying-rewetting stress on bacterioplankton in the light of the stress history and the rate and timing of dispersal after the rewetting. We found that the drying phase resulted mainly in a change of function, whereas the complete desiccation and rewetting processes strongly affected both composition and function, which were, however, influenced by the initial conditions and stress history of the communities. Effects of dispersal were generally stronger when it occurred at an early stage after the rewetting. At this stage, selective establishment of dispersed bacteria coupled with enhanced compositional and functional recovery was found, whereas effects of dispersal were neutral, that is, predictable by dispersal rates, at later stages. Our studies therefore show that both the stress history and the timing of dispersal are important factors that influence the response of bacterial communities to environmental change and stress events.

Modern molecular approaches for analyzing microbial diversity from mushroom compost ecosystem

Biosphere is a store house of various microorganisms that may be employed to isolate and exploit microbes for environmental, pharmaceutical, agricultural and industrial applications. There is restricted data regarding the structure and dynamics of microbial communities in several ecosystems because only a little fraction of microbial diversity is accessible by culture methods. Owing to limitations of traditional enrichment methods and pure culture techniques, microbiological studies have offered a narrow portal for investigating microbial flora. The bacterial community represented by the morphological and nutritional criteria failed to provide a natural taxonomic order according to the evolutionary relationship. Genetic diversity among the isolates recovered from mushroom compost has not been widely studied. To understand genetic diversity and community composition of the mushroom compost microflora, different approaches are now followed by taxonomists, to characterize and identify isolates up to species level. Molecular microbial ecology is an emerging discipline of biology under molecular approach which can provide complex community profiles along with useful phylogenetic information. The genomic era has resulted in the development of new molecular tools and techniques for study of culturable microbial diversity including the DNA base ratio (mole% G + C), DNA-DNA hybridization, DNA microarray and reverse sample genome probing. In addition, non-culturable diversity of mushroom compost ecosystem can be characterized by employing various molecular tools which would be discussed in the present review.

Application of special oligotrophic media for cultivation of bacterial communities originated from ultrapure water

Because of the selectivity of the commonly used media it is very difficult to cultivate bacteria inhabiting ultrapure waters under laboratory conditions. In this study 5 new media (synthetic and complex) were developed to reveal bacterial community of the ultrapure water originated from the water purification system of a Hungarian power plant which was studied already with using traditional media. Composition of the new media tends to reproduce the nutrient deficient conditions of the investigated water, therefore media were highly oligotrophic. Altogether 122 bacterial strains were isolated from the 5 different media. Based on ARDRA grouping 27 strains were chosen for the partial 16S rRNA gene sequence analysis. The results showed that the applied media strongly influence the composition of the cultivable bacterial community. A larger scale of α-Proteobacteria (Mesorhizobium spp., Ancylobacter sp., Methylobacterium sp.) and many Actinobacteria (Leifsonia sp., Microbacterium spp., Mycobacterium spp.) could be isolated from the same ultrapure water system than with any other cultivation methods or media applied before. Moreover, two novel bacterial taxa could be isolated from the studied water purification system.

Depletion of unwanted nucleic acid templates by selective cleavage: LNAzymes, catalytically active oligonucleotides containing locked nucleic acids, open a new window for detecting rare microbial community members

Many studies of molecular microbial ecology rely on the characterization of microbial communities by PCR amplification, cloning, sequencing, and phylogenetic analysis of genes encoding rRNAs or functional marker enzymes. However, if the established clone libraries are dominated by one or a few sequence types, the cloned diversity is difficult to analyze by random clone sequencing. Here we present a novel approach to deplete unwanted sequence types from complex nucleic acid mixtures prior to cloning and downstream analyses. It employs catalytically active oligonucleotides containing locked nucleic acids (LNAzymes) for the specific cleavage of selected RNA targets. When combined with in vitro transcription and reverse transcriptase PCR, this LNAzyme-based technique can be used with DNA or RNA extracts from microbial communities. The simultaneous application of more than one specific LNAzyme allows the concurrent depletion of different sequence types from the same nucleic acid preparation. This new method was evaluated with defined mixtures of cloned 16S rRNA genes and then used to identify accompanying bacteria in an enrichment culture dominated by the nitrite oxidizer "Candidatus Nitrospira defluvii." In silico analysis revealed that the majority of publicly deposited rRNA-targeted oligonucleotide probes may be used as specific LNAzymes with no or only minor sequence modifications. This efficient and cost-effective approach will greatly facilitate tasks such as the identification of microbial symbionts in nucleic acid preparations dominated by plastid or mitochondrial rRNA genes from eukaryotic hosts, the detection of contaminants in microbial cultures, and the analysis of rare organisms in microbial communities of highly uneven composition.

Mechanisms determining the fate of dispersed bacterial communities in new environments

Recent work has shown that dispersal has an important role in shaping microbial communities. However, little is known about how dispersed bacteria cope with new environmental conditions and how they compete with local resident communities. To test this, we implemented two full-factorial transplant experiments with bacterial communities originating from two sources (freshwater or saline water), which were incubated, separately or in mixes, under both environmental conditions. Thus, we were able to separately test for the effects of the new environment with and without interactions with local communities. We determined community composition using 454-pyrosequencing of bacterial 16S rRNA to specifically target the active fraction of the communities, and measured several functional parameters. In absence of a local resident community, the net functional response was mainly affected by the environmental conditions, suggesting successful functional adaptation to the new environmental conditions. Community composition was influenced both by the source and the incubation environment, suggesting simultaneous effects of species sorting and functional plasticity. In presence of a local resident community, functional parameters were higher compared with those expected from proportional mixes of the unmixed communities in three out of four cases. This was accompanied by an increase in the relative abundance of generalists, suggesting that competitive interactions among local and immigrant taxa could explain the observed 'functional overachievement'. In summary, our results suggest that environmental filtering, functional plasticity and competition are all important mechanisms influencing the fate of dispersed communities.

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 independent methods. Our results showed increased CFU and direct cell counts after the storage. Cultivation results showed the dominance of aerobic, chemoorganotrophic α-Proteobacteria in both samples. In case of TKU sample, a more complex bacterial community structure could be detected. The applied molecular method (T-RFLP) indicated the presence of a complex microbial community structure with changes in the taxon composition: while in the inlet water sample (TKE) α-Proteobacteria (Sphingomonas sp., Novosphingobium hassiacum) dominated, in the outlet water sample (TKU) the bacterial community shifted towards the dominance of α-Proteobacteria (Rhodoferax sp., Polynucleobacter sp., Sterolibacter sp.), CFB (Bacteroidetes, formerly Cytophaga-Flavobacterium-Bacteroides group) and Firmicutes. This shift to the direction of fermentative communities suggests that storage could help the development of communities with an increased tendency toward corrosion.

Bacterial communities in the gut of the freshwater copepod Eudiaptomus gracilis

Eudiaptomus gracilis is the most abundant member of the zooplankton, plays a key role in the food web of Lake Balaton (Hungary). In the present study the composition of bacterial communities of this copepod was investigated based on cultivation and molecular cloning. The cultivated bacterial strains from the gut homogenate samples of Eudiaptomus gracilis belonged to four different clades: Firmicutes, Actinobacteria, Bacteriodetes and Proteobacteria. Clone library showed high species diversity, Firmicutes, Actinobacteria, Proteobacteria, representatives of Deinococcus-Thermus lineage and Cyanobacteria were detected. The isolated strains were very effective in degradation of different biopolymers. Many of the detected bacteria are known as opportunistic human or fish pathogens (Pseudomonas spp., Aeromonas spp., Chryseobacterium sp. and Staphylococcus sp.).

Microbiological investigation of an industrial ultra pure supply water plant using cultivation-based and cultivation-independent methods

Ultra pure waters (UPW), characterized by extremely low salt and nutrient concentrations, can suffer from microbial contamination which causes biofouling and biocorrosion, possibly leading to reduced lifetime and increased operational costs. Samples were taken from an ultra pure supply water producing plant of a power plant. Scanning electron microscopic examination was carried out on the biofilms formed in the system. Biofilm, ion exchange resin, and water samples were characterized by culture-based methods and molecular fingerprinting (terminal restriction fragment length polymorphism [T-RFLP] analysis and molecular cloning). Identification of bacteria was based on 16S rDNA sequence comparison. A complex microbial community structure was revealed. Nearly 46% of the clones were related to as yet uncultured bacteria. The community profiles of the water samples were the most diverse and most of bacteria were recruited from bacterial communities of tube surface and ion exchange resin biofilms. Microbiota of different layers of the mixed bed ion exchange resin showed the highest similarity. Most of the identified taxa (dominated by β-Proteobacteria) could take part in microbially influenced corrosion.

Tetrachloroethene conversion to ethene by a Dehalococcoides-containing enrichment culture from Bitterfeld

A Dehalococcoides-dominated culture coupling reductive dechlorination of tetrachloroethene (PCE) to ethene to growth was enriched from a European field site for the first time. Microcosms were set up using groundwater from a chlorinated ethene-contaminated anaerobic aquifer in Bitterfeld (Germany). Active, lactate-amended microcosms capable of PCE dechlorination to ethene without the accumulation of intermediates were used for further enrichment. After three transfers on lactate as an electron donor and PCE as an electron acceptor, the enrichment was transferred to parallel cultures with one of the chlorinated ethenes as an electron acceptor and acetate and hydrogen as the carbon and energy source, respectively. After three more transfers, a highly purified culture was derived that was capable of dechlorinating PCE with hydrogen and acetate as the electron donor and carbon source, respectively. PCR, followed by denaturing gradient gel electrophoresis, cloning and sequencing revealed that this culture was dominated by a Dehalococcoides sp. belonging to the Pinellas group. Investigation of substrate specificity in the parallel cultures suggested the presence of a novel Dehalococcoides that can couple all dechlorination steps, from PCE to ethene, to energy conservation. Quantitative real-time PCR confirmed growth with PCE, cis-dichloroethene, 1,1-dichloroethene or vinyl chloride as electron acceptors. The culture was designated BTF08 due to its origin in Bitterfeld.

Elucidating MTBE degradation in a mixed consortium using a multidisciplinary approach

The structure and function of a microbial community capable of biodegrading methyl-tert-butyl ether (MTBE) was characterized using compound-specific stable isotope analysis (CSIA), clone libraries and stable isotope probing of proteins (Protein-SIP). The enrichment culture (US3-M), which originated from a gasoline-impacted site in the United States, has been enriched on MTBE as the sole carbon source. The slope of isotopic enrichment factors (epsilon(C) of -2.29+/-0.03 per thousand; epsilon(H) of -58+/-6 per thousand) for carbon and hydrogen discrimination (Deltadelta(2)H/Deltadelta(13)C) was on average equal to Lambda=24+/-2, a value closely related to the reaction mechanism of MTBE degradation in Methylibium petroleiphilum PM1. 16S rRNA gene libraries revealed sequences belonging to M. petroleiphilum PM1, Hydrogenophaga sp., Thiothrix unzii, Rhodobacter sp., Nocardiodes sp. and different Sphingomonadaceae bacteria. Protein-SIP analysis of the culture grown on (13)C-MTBE as the only carbon source revealed that proteins related to members of the Comamonadaceae family, such as Delftia acidovorans, Acidovorax sp. or Comamonas sp., were not (13)C-enriched, whereas proteins related to M. petroleiphilum PM1 showed an average incorporation of 94.5 atom%(13)C. These results indicate a key role for this species in the degradation of MTBE within the US3-M consortia. The combination of CSIA, molecular biology and Protein-SIP facilitated the analysis of an MTBE-degrading mixed culture from a functional and phylogenetic point of view.

Antibacterial effect of bactericide immobilized in resin matrix

OBJECTIVE

Biomaterials with anti-microbial properties are highly desirable in the oral cavity. Ideally, bactericidal molecules should be immobilized within the biomaterial to avoid unwanted side-effects against surrounding tissues. They may then however loose much of their antibacterial efficiency. The aim of this study was to investigate how much antibacterial effect an immobilized bactericidal molecule still has against oral bacteria.

METHODS

Experimental resins containing 0, 1 and 3% cetylpyridinium chloride (CPC) were polymerized, and the bacteriostatic and bactericidal effects against Streptococcus mutans were determined. Adherent S. mutans on HAp was quantitatively determined using FE-SEM and living cells of S. mutans were quantified using real-time RT-PCR. The amount of CPC released from the 0%-, 1%- and 3%-CPC resin sample into water was spectrometrically quantified using a UV-vis recording spectrophotometer.

RESULTS

UV spectrometry revealed that less than 0.11 ppm of CPC was released from the resin into water for all specimens, which is lower than the minimal concentration generally needed to inhibit biofilm formation. Growth of S. mutans was significantly inhibited on the surface of the 3%-CPC-containing resin coating, although no inhibitory effect was observed on bacteria that were not in contact with its surface. When immersed in water, the antibacterial capability of 3%-CPC resin lasted for 7 days, as compared to resin that did not contain CPC.

SIGNIFICANCE

These results demonstrated that the bactericidal molecule still possessed significant contact bacteriostatic activity when it was immobilized in the resin matrix.

A bacterial population study of commercialized wastewater inoculants

AIMS

To assess the bacterial diversity and safety of wastewater inoculants, which are commercially available products used to improve the aerobic digestion processes of the domestic waste compost in the septic tank.

METHODS AND RESULTS

Eighteen wastewater inoculants were analysed on nonselective and selective media and the cultivable bacteria were identified. In all wastewater inoculants, the number of CFUs were between 10(4) and 10(7) g(-1) powder on nonselective media and Bacillus was the predominant cultivable genus. Culture-independent molecular methods such as sequencing of 16S rRNA clone libraries and denaturating gradient gel electrophoresis demonstrated the high prevalence of interfering chloroplast 16S rRNA from plant material and the presence of Bacillus spp. Only after selective enrichments and cultivation, the presence of one pathogenic strain (Klebsiella pneumoniae subsp. pneumoniae) and one opportunistic strain of (Enterobacter cloacae) bacteria were detected in six different products.

CONCLUSION

The predominant cultivable species of the wastewater inoculants were Bacillus spp. and after enrichment six products were found to contain opportunistic or pathogenic strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

The presence of opportunistic pathogenic strains in the inoculants might represent a risk for immunocompromised, the elderly or children. A clear labelling should therefore be displayed on the product.

Comparison of phenotypic and genotypic methods for the detection of environmental isolates of Pseudomonas aeruginosa

During remediation processes, biological monitoring should be generally required. Hydrocarbon contaminated soils may provide favorable conditions for several opportunistic pathogenic microorganisms, thereby increasing their populations over risky levels. Therefore, during remediation processes of the subsurface medium biological monitoring is of prime importance. The accuracy, time and cost efficiency of the relevant identification method are major factors while monitoring these microbes. During previous years (2002-05), we collected 68 soil samples from 17 different oil contaminated sites, such as petrol stations, airfields and pipeline-breaks. We compared frequently applied detection methods of Pseudomonas aeruginosa, both traditional microbiological and molecular biological techniques, on 43 environmental isolates originating from these sites. The following methods were subjected to comparative analysis: (i) the Hungarian Standard method; (ii) the method described in "The Prokaryotes" handbook; (iii) the API 20NE biochemical fingerprinting, as well as PCR protocols aimed to amplify; (iv) the exotoxin-A gene; and (v) the 16S rDNA variable regions V2 and V8. In five cases, phenotypic methods gave false-negative results. 16S rDNA sequence analysis was done to confirm the identity of these five strains, which verified the results of molecular methods. In addition, faults were found in the evaluation of the originally described ETA PCR protocol, which was corrected by us.

Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis

In the attempt to explore complex bacterial communities of environmental samples, primers hybridizing to phylogenetically highly conserved regions of 16S rRNA genes are widely used, but differential amplification is a recognized problem. The biases associated with preferential amplification of multitemplate PCR were investigated using 'universal' bacteria-specific primers, focusing on the effect of primer mismatch, annealing temperature and PCR cycle number. The distortion of the template-to-product ratio was measured using predefined template mixtures and environmental samples by terminal restriction fragment length polymorphism analysis. When a 1 : 1 genomic DNA template mixture of two strains was used, primer mismatches inherent in the 63F primer presented a serious bias, showing preferential amplification of the template containing the perfectly matching sequence. The extent of the preferential amplification showed an almost exponential relation with increasing annealing temperature from 47 to 61 degrees C. No negative effect of the various annealing temperatures was observed with the 27F primer, with no mismatches with the target sequences. The number of PCR cycles had little influence on the template-to-product ratios. As a result of additional tests on environmental samples, the use of a low annealing temperature is recommended in order to significantly reduce preferential amplification while maintaining the specificity of PCR.

A molecular approach to identify active microbes in environmental eukaryote clone libraries

A rapid method for the simultaneous extraction of RNA and DNA from eukaryote plankton samples was developed in order to discriminate between indigenous active cells and signals from inactive or even dead organisms. The method was tested using samples from below the chemocline of an anoxic Danish fjord. The simple protocol yielded RNA and DNA of a purity suitable for amplification by reverse transcription-polymerase chain reaction (RT-PCR) and PCR, respectively. We constructed an rRNA-derived and an rDNA-derived clone library to assess the composition of the microeukaryote assemblage under study and to identify physiologically active constituents of the community. We retrieved nearly 600 protistan target clones, which grouped into 84 different phylotypes (98% sequence similarity). Of these phylotypes, 27% occurred in both libraries, 25% exclusively in the rRNA library, and 48% exclusively in the rDNA library. Both libraries revealed good correspondence of the general community composition in terms of higher taxonomic ranks. They were dominated by anaerobic ciliates and heterotrophic stramenopile flagellates thriving below the fjord's chemocline. The high abundance of these bacterivore organisms points out their role as a major trophic link in anoxic marine systems. A comparison of the two libraries identified phototrophic dinoflagellates, "uncultured marine alveolates group I," and different parasites, which were exclusively detected with the rDNA-derived library, as nonindigenous members of the anoxic microeukaryote community under study.

Suicide polymerase endonuclease restriction, a novel technique for enhancing PCR amplification of minor DNA templates

PCR-based molecular analyses can be hindered by the presence of unwanted or dominant DNA templates that reduce or eliminate detection of alternate templates. We describe here a reaction in which such templates can be exclusively digested by endonuclease restriction, leaving all other DNAs unmodified. After such a modification, the digested template is no longer available for PCR amplification, while nontarget DNAs remain intact and can be amplified. We demonstrate the application of this method and use denaturing gradient gel electrophoresis to ascertain the removal of target DNA templates and the subsequent enhanced amplification of nondigested DNAs. Specifically, plastid 16S rRNA genes were exclusively digested from environmental DNA extracted from plant roots. In addition, pure culture and environmental DNA extracts were spiked with various amounts of genomic DNA extracted from Streptomyces spp., and selective restriction of the Streptomyces 16S rRNA genes via the suicide polymerase endonuclease restriction PCR method was employed to remove the amended DNA.

Molecular characterization of dichloromethane-degrading Hyphomicrobium strains using 16S rDNA and DCM dehalogenase gene sequences

A phylogenetic analysis of 6 strains of dichloromethane (DCM) utilizing bacteria was performed. Based on the almost complete 16S rDNA sequence determination, all strains clustered together and showed high sequence similarity to Hyphomicrobium denitrificans, except for the strain MC8b, which is only moderately related to them and probably represents a distinct species. The 16S rDNA-based phylogenetic tree was compared to the one obtained from the DNA sequence data of the dcmA gene coding DCM dehalogenase, the key enzyme of DCM utilization. The topology of the two trees is in good agreement and may suggest an ancient origin of DCM dehalogenase, but also raises questions about the original role of the enzyme.

Effect of plants and filter materials on bacteria removal in pilot-scale constructed wetlands

Due to the lack of testing units or appropriate experimental approaches, only little is known about the removal of bacteria in constructed wetlands. However, improved performance in terms of water sanitation requires a detailed understanding of the ongoing processes. Therefore, we analyzed the microbial diversity and the survival of Enterobacteriaceae in six pilot-scale constructed wetland systems treating domestic wastewater: two vertical sand filters, two vertical expanded clay filters and two horizontal sand filters (each planted and unplanted). Samples were taken from the in- and outflow, from the rhizosphere, and from the bulk soil at various depths. Colony-forming units of heterotrophic bacteria and coliforms were analyzed and the removal of bacteria between the in- and outflow was determined to within 1.5-2.5 orders of magnitude. To access the taxon-specific biodiversity of potential pathogens in the filters and to reduce the complexity of the analysis, specific primers for Enterobacteriaceae were developed. While performing PCR-SSCP analyses, a pronounced decrease in diversity from the inflow to the outflow of treated wastewater was observed. No differences were observed between the bulk soil of planted and unplanted vertical filters. Some bands appeared in the rhizosphere that were not present in the bulk soil, indicating the development of specific communities stimulated by the plants. The fingerprinting of the rhizosphere of plants grown on sand or expanded clay exhibited many differences, which show that different microbial communities exist depending on the soil type of the filters. The use of the taxon-specific primers enabled us to evaluate the fate of the Enterobacteriaceae entering the wetlands and to localize harboring in the rhizosphere. The most abundant bands of the profiles were sequenced: Pantoea agglomerans was found in nearly all samples from the soil but not in the effluent, whereas Citrobacter sp. could not be removed by the horizontal unplanted sand and vertical planted expanded clay filters. These results show that the community in wetland system is strongly influenced by the filtration process, the filter material and the plants.

Baktériumok és gombák kolonizációja génmódosított (Bt-) és izogénes kontroll kukorica rizoszférájában

A Bacillus thuringiensiscry1Ab endotoxint termelő transzgénikus kukorica (DK440BTY) és izogénes, toxint nem termelő kukorica (DK440) rizoszféráját jellemeztük talajbiológiai eszközökkel, illetve összehasonlító értékelést végeztünk egy vegetációs periódus három mintavételi időszakában. Telepszámlálásos módszerrel meghatároztuk néhány kitenyészthető mikrobacsoport (heterotrófok, oligotrófok, spórás mikrooganizmusok, szabadon élő N2-kötők és mikroszkopikus gombák) csíraszámát a rizoszféra talajában. Elvégeztük a mikrobiális össz-aktivitás vizsgálatát fluoreszcein-diacetát (FDA) hidrolízisének mérésével, illetve nyomon követtük a gyökérrendszer szimbiotikus struktúráinak, azaz az arbuszkuláris mikorrhiza gombák kolonizációjának a működőképességét is. A rizoszférához szorosan kapcsolódó talajrészben a szabadon élő szaprotróf Trichoderma gombák faji diverzitásának az alakulását ellenőriztük.  Megállapítottuk, hogy a belső rizoszféra (endoriza) mikroszimbiontás kolonizációja az első mintavétel során (2001. június) szignifikánsan kisebb aktivitást mutatott, és csökkent a gomba működőképességét jelző arbuszkulumok mennyisége is. A további mintavételek során (2001. augusztus és október) azonban ezek a különbségek nem jelentkeztek, a szimbiózis működőképessége helyreállt. A varianciaanalízis azonban összesített hatásban szignifikáns különbséget jelzett. A gyökérfelszín kitenyészthető mikrobacsoportjainak csíraszámában nem adódott statisztikailag igazolható különbség a kétféle növény között. Az FDA módszerrel kimutatható össz-mikrobiális aktivitást ugyanakkor mindegyik mintavételnél nagyobbnak találtuk a Bt-kukorica rizoszférájában, amiből a fiziológiai tulajdonságok megváltozására következtettünk. A transzgénikus növény gyökérhatásának távolabbi részén, a külső rizoszférában a Trichodema gombák száma és faji összetétele csak szezonális változásokat mutatott, de nem különbözött szignifikánsan a génmódosított növénynél. Eredményeink jelzik a génmódosítás közvetett hatását a rizoszférában található „nem célzott” szervezetek összetételére vagy aktivitására, és felhívják a figyelmet a további, tartamjellegű vizsgálatok szükségességére is. 

Observation of bias associated with re-amplification of DNA isolated from denaturing gradient gels

DNA from environmental PCR products separated by denaturing gradient gel electrophoresis (DGGE) was isolated from the background smear rather than from discrete bands of the DGGE gel. The "interband" region was considered as a potential source of less dominant members of natural microbial communities. Surprisingly, instead of detecting new bands from the re-amplified PCR products, patterns very similar to the original ones were obtained regardless of the position of the "interband" region. The results suggest that the separation of amplicons by DGGE may not be perfect and band re-amplification based sequence analyses need careful interpretation.