Home About us Contact
|
Home About us Contact | ||
|
|
||
rRNA Gene Fragments (rrna + gene_fragment)
Selected AbstractsQuantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugationENVIRONMENTAL MICROBIOLOGY, Issue 7 2001Sophie Courtois All molecular analyses of soil bacterial diversity are based on the extraction of a representative fraction of cellular DNA. Methods of DNA extraction for this purpose are divided into two categories: those in which cells are lysed within the soil (direct extraction) and those in which cells are first removed from soil (cell extraction) and then lysed. The purpose of this study was to compare a method of direct extraction with a method in which cells were first separated from the soil matrix by Nycodenz gradient centrifugation in order to evaluate the effect of these different approaches on the analysis of the spectrum of diversity in a microbial community. We used a method based on polymerase chain reaction (PCR) amplification of a 16S rRNA gene fragment, followed by hybridization of the amplified fragments to a set of specific probes to assess the phylogenetic diversity of our samples. Control parameters, such as the relationship between amount of DNA template and amount of PCR product and the influence of competing DNA on PCR amplification, were first examined. Comparison between extraction methods showed that less DNA was extracted when cells were first separated from the soil matrix (0.4 µg g,1 dry weight soil versus 38,93 µg g,1 obtained by in situ lysis methods). However, with the exception of the ,-subclass of Proteobacteria, there was no significant difference in the spectrum of diversity resulting from the two extraction strategies. [source] Molecular identification of five commercial flatfish species by PCR,RFLP analysis of a 12S rRNA gene fragmentJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 8 2003Angel S Comesaña Abstract Refrigerated or frozen fillets of commercial flatfish species are sometimes mislabelled, and identification of those products is needed to avoid fraudulent substitution. Molecular identification of five commercial flatfish species (order Pleuronectiformes), ie Lepidorhombus whiffiagonis (megrim), Platichthys flesus (flounder), Reinhardtius hippoglossoides (Greenland halibut), Scophthalmus maximus (turbot) and Solea vulgaris (= S solea) (sole), has been carried out on the basis of the amplification of an approximately 433 bp segment from the mitochondrial 12S rRNA gene using the polymerase chain reaction (PCR) and universal primers. Direct DNA sequencing from two PCR products for each flatfish species was carried out, and sequences were used to select six restriction enzymes. PCR products of 15 individuals of each species were cut with each enzyme, resulting in species-specific restriction fragment length polymorphism (RFLP). The five flatfish species could be identified by application of the restriction enzyme AluI as well as by using different combinations of a pair of enzymes, ie DdeI and either AciI or MwoI. No intraspecific genetic polymorphism was found for any of the six enzymes. Results confirmed the usefulness of this technique to distinguish and genetically characterise refrigerated or frozen pieces of these five flatfish species. Copyright © 2003 Society of Chemical Industry [source] A new species of Syntretus Foerster (Hymenoptera: Braconidae: Euphorinae), a parasitoid of the stingless bee Trigona carbonaria Smith (Hymenoptera: Apidae: Meliponinae)AUSTRALIAN JOURNAL OF ENTOMOLOGY, Issue 1 2009Rosalyn Gloag Abstract A new species of euphorine braconid, Syntretus trigonaphagus sp. nov., is described and illustrated. This is the first Australian Syntretus species to be described and the first record of braconids parasitising Trigona Jurine stingless bees. Egg-laying by adults and emergence of larvae from the host Trigona carbonaria is detailed. A 12S ribosomal rRNA gene fragment was sequenced to confirm the association of larvae and adults of the wasp parasitoid. [source] Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern OceanENVIRONMENTAL MICROBIOLOGY, Issue 8 2009Helge-Ansgar Giebel Summary We assessed the composition of the bacterioplankton in the Atlantic sector of the Southern Ocean in austral fall and winter and in New Zealand coastal waters in summer. The various water masses between the subtropics/Agulhas,Benguela boundary region and the Antarctic coastal current exhibited distinct bacterioplankton communities with the highest richness in the polar frontal region, as shown by denaturing gradient gel electrophoresis of 16S rRNA gene fragments. The SAR11 clade and the Roseobacter clade-affiliated (RCA) cluster were quantified by real-time quantitative PCR. SAR11 was detected in all samples analysed from subtropical waters to the coastal current and to depths of > 1000 m. In fall and winter, this clade constituted < 3% to 48% and 4,28% of total bacterial 16S rRNA genes respectively, with highest fractions in subtropical to polar frontal regions. The RCA cluster was only present in New Zealand coastal surface waters not exceeding 17°C, in the Agulhas,Benguela boundary region (visited only during the winter cruise), in subantarctic waters and in the Southern Ocean. In fall, this cluster constituted up to 36% of total bacterial 16S rRNA genes with highest fractions in the Antarctic coastal current and outnumbered the SAR11 clade at most stations in the polar frontal region and further south. In winter, the RCA cluster constituted lower proportions than the SAR11 clade and did not exceed 8% of total bacterial 16S rRNA genes. In fall, the RCA cluster exhibited significant positive correlations with latitude and ammonium concentrations and negative correlations with concentrations of nitrate, phosphate, and for near-surface samples also with chlorophyll a, biomass production of heterotrophic prokaryotes and glucose turnover rates. The findings show that the various water masses between the subtropics and the Antarctic coastal current harbour distinct bacterioplankton communities. They further indicate that the RCA cluster, despite the narrow sequence similarity of > 98% of its 16S rRNA gene, is an abundant component of the heterotrophic bacterioplankton in the Southern Ocean, in particular in its coldest regions. [source] The role of Variovorax and other Comamonadaceae in sulfur transformations by microbial wheat rhizosphere communities exposed to different sulfur fertilization regimesENVIRONMENTAL MICROBIOLOGY, Issue 6 2008Achim Schmalenberger Summary Sulfonates are a key component of the sulfur present in agricultural soils. Their mobilization as part of the soil sulfur cycle is mediated by rhizobacteria, and involves the oxidoreductase AsfA. In this study, the effect of fertilization regime on rhizosphere bacterial asfA distribution was examined at the Broadbalk long-term wheat experiment, Rothamsted, UK, which was established in 1843, and has included a sulfur-free treatment since 2001. Direct isolation of desulfonating rhizobacteria from the wheat rhizospheres led to the identification of several Variovorax and Polaromonas strains, all of which contained the asfA gene. Rhizosphere DNA was isolated from wheat rhizospheres in plots fertilized with inorganic fertilizer with and without sulfur, with farmyard manure or from unfertilized plots. Genetic profiling of 16S rRNA gene fragments [denaturing gradient gel electrophoresis (DGGE)] from the wheat rhizospheres revealed that the level of inorganic sulfate in the inorganic fertilizer was correlated with changes in the general bacterial community structure and the betaproteobacterial community structure in particular. Community analysis at the functional gene level (asfA) showed that 40% of clones in asfAB clone libraries were affiliated to the genus Variovorax. Analysis of asfAB -based terminal restriction fragment length polymorphism (T-RFLP) fingerprints showed considerable differences between sulfate-free treatments and those where sulfate was applied. The results suggest the occurrence of desulfonating bacterial communities that are specific to the fertilization regime chosen and that arylsulfonates play an important role in rhizobacterial sulfur nutrition. [source] Diversity of phototrophic bacteria in microbial mats from Arctic hot springs (Greenland)ENVIRONMENTAL MICROBIOLOGY, Issue 1 2007Guus Roeselers Summary We investigated the genotypic diversity of oxygenic and anoxygenic phototrophic microorganisms in microbial mat samples collected from three hot spring localities on the east coast of Greenland. These hot springs harbour unique Arctic microbial ecosystems that have never been studied in detail before. Specific oligonucleotide primers for cyanobacteria, purple sulfur bacteria, green sulfur bacteria and Choroflexus/Roseiflexus -like green non-sulfur bacteria were used for the selective amplification of 16S rRNA gene fragments. Amplification products were separated by denaturing gradient gel electrophoresis (DGGE) and sequenced. In addition, several cyanobacteria were isolated from the mat samples, and classified morphologically and by 16S rRNA-based methods. The cyanobacterial 16S rRNA sequences obtained from DGGE represented a diverse, polyphyletic collection of cyanobacteria. The microbial mat communities were dominated by heterocystous and non-heterocystous filamentous cyanobacteria. Our results indicate that the cyanobacterial community composition in the samples were different for each sampling site. Different layers of the same heterogeneous mat often contained distinct and different communities of cyanobacteria. We observed a relationship between the cyanobacterial community composition and the in situ temperatures of different mat parts. The Greenland mats exhibited a low diversity of anoxygenic phototrophs as compared with other hot spring mats which is possibly related to the photochemical conditions within the mats resulting from the Arctic light regime. [source] Cultivation-independent analysis of Pseudomonas species in soil and in the rhizosphere of field-grown Verticillium dahliae host plantsENVIRONMENTAL MICROBIOLOGY, Issue 12 2006Rodrigo Costa Summary Despite their importance for rhizosphere functioning, rhizobacterial Pseudomonas spp. have been mainly studied in a cultivation-based manner. In this study a cultivation-independent method was used to determine to what extent the factors plant species, sampling site and year-to-year variation influence Pseudomonas community structure in bulk soil and in the rhizosphere of two Verticillium dahliae host plants, oilseed rape and strawberry. Community DNA was extracted from bulk and rhizosphere soil samples of flowering plants collected at three different sites in Germany in two consecutive years. Pseudomonas community structure and diversity were assessed using a polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) system to fingerprint Pseudomonas -specific 16S rRNA gene fragments amplified from community DNA. Dominant and differentiating DGGE bands were excised from the gels, cloned and sequenced. The factors sampling site, plant species and year-to-year variation were shown to significantly influence the community structure of Pseudomonas in rhizosphere soils. The composition of Pseudomonas 16S rRNA gene fragments in the rhizosphere differed from that in the adjacent bulk soil and the rhizosphere effect tended to be plant-specific. The clone sequences of most dominant bands analysed belonged to the Pseudomonas fluorescens lineage and showed closest similarity to culturable Pseudomonas known for displaying antifungal properties. This report provides a better understanding of how different factors drive Pseudomonas community structure and diversity in bulk and rhizosphere soils. [source] Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater,marine gradientENVIRONMENTAL MICROBIOLOGY, Issue 4 2006Thomas E. Freitag Summary To determine whether the distribution of estuarine ammonia-oxidizing bacteria (AOB) was influenced by salinity, the community structure of betaproteobacterial ammonia oxidizers (AOB) was characterized along a salinity gradient in sediments of the Ythan estuary, on the east coast of Scotland, UK, by denaturant gradient gel electrophoresis (DGGE), cloning and sequencing of 16S rRNA gene fragments. Ammonia-oxidizing bacteria communities at sampling sites with strongest marine influence were dominated by Nitrosospira cluster 1-like sequences and those with strongest freshwater influence were dominated by Nitrosomonas oligotropha- like sequences. Nitrosomonas sp. Nm143 was the prevailing sequence type in communities at intermediate brackish sites. Diversity indices of AOB communities were similar at marine- and freshwater-influenced sites and did not indicate lower species diversity at intermediate brackish sites. The presence of sequences highly similar to the halophilic Nitrosomonas marina and the freshwater strain Nitrosomonas oligotropha at identical sampling sites indicates that AOB communities in the estuary are adapted to a range of salinities, while individual strains may be active at different salinities. Ammonia-oxidizing bacteria communities that were dominated by Nitrosospira cluster 1 sequence types, for which no cultured representative exists, were subjected to stable isotope probing (SIP) with 13C-HCO3,, to label the nucleic acids of active autotrophic nitrifiers. Analysis of 13C-associated 16S rRNA gene fragments, following CsCl density centrifugation, by cloning and DGGE indicated sequences highly similar to the AOB Nitrosomonas sp. Nm143 and Nitrosomonas cryotolerans and to the nitrite oxidizer Nitrospira marina. No sequence with similarity to the Nitrosospira cluster 1 clade was recovered during SIP analysis. The potential role of Nitrosospira cluster 1 in autotrophic ammonia oxidation therefore remains uncertain. [source] Marine diatom species harbour distinct bacterial communitiesENVIRONMENTAL MICROBIOLOGY, Issue 6 2005Hans-Peter Grossart Summary We examined bacterial dynamics in batch cultures of two axenic marine diatoms (Thalassiosira rotula and Skeletonema costatum). The axenic diatoms were inoculated with natural bacterial assemblages and monitored by 4,6-diamidino-2-phenolindole (DAPI) counts, denaturing gradient gel electrophoresis (DGGE) with subsequent analysis of excised, sequenced 16S rRNA gene fragments, and fluorescence in situ hybridization (FISH) with group-specific 16S rRNA oligonucleotide probes. Our results show that algal growth exhibited pronounced differences in axenic treatments and when bacteria were present. Bacterial abundance and community structure greatly depended on species, growth and physiological status of even closely related algae. Free-living and phytoplankton-associated bacteria were very different from each other and were dominated by distinct phylogenetic groups. The diatom-associated bacteria mainly belonged to the Flavobacteria,Sphingobacteria group of the Bacteroidetes phylum whereas free-living bacteria, which were rather similar in both cultures, comprised mainly of members of the Roseobacter,group ,of ,,- Proteobacteria. ,Presence and disappearance of specific bacteria during algal growth indicated pronounced differences in environmental conditions over time and selection of bacteria highly adapted to the changing conditions. Tight interactions between marine bacteria and diatoms appear to be important for the decomposition of organic matter and nutrient cycling in the sea. [source] The impact of grassland management on archaeal community structure in upland pasture rhizosphere soilENVIRONMENTAL MICROBIOLOGY, Issue 3 2003Graeme W. Nicol Summary The community structure of rhizosphere soil Archaea from three grassland types, associated with different management practices, was examined at a site in the Borders region of Scotland, by analysis of 16S rRNA gene fragments amplified from 16S rDNA and from rRNA. Denaturing gradient gel electrophoresis (DGGE) and sequence analysis of amplified products indicated high relative abundance within the archaeal community of two distinct lineages of non-thermophilic (group 1) Crenarchaeota. Grassland management practices influenced archaeal community structure, as characterized by both 16S rRNA- and 16S rDNA-derived DGGE profiles. One band dominated DGGE profiles in all three grassland types examined, and reproducible differences in the presence and intensity of bands were observed between profiles from managed and natural grassland sites. Analysis of 16S rRNA-derived amplicons from managed and natural grasslands at sites in the north of England and the north of Wales also indicated high relative abundance of non-thermophilic crenarchaeotes within the archaeal community. The band dominating the Scottish grassland site also dominated DGGE profiles from the English and Welsh sites, and similar differences were seen between profiles derived from soils subjected to different management regimes. The study indicates that grassland archaeal communities are dominated by Crenarchaeota, with closely related members of this lineage ubiquitous in distribution in UK upland pasture, and indicate that management practices influence the nature of the crenarchaeotal community. [source] Methane assimilation and trophic interactions with marine Methylomicrobium in deep-water coral reef sediment off the coast of NorwayFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Sigmund Jensen Abstract Deep-water coral reefs are seafloor environments with diverse biological communities surrounded by cold permanent darkness. Sources of energy and carbon for the nourishment of these reefs are presently unclear. We investigated one aspect of the food web using DNA stable-isotope probing (DNA-SIP). Sediment from beneath a Lophelia pertusa reef off the coast of Norway was incubated until assimilation of 5 ,mol 13CH4 g,1 wet weight occurred. Extracted DNA was separated into ,light' and ,heavy' fractions for analysis of labelling. Bacterial community fingerprinting of PCR-amplified 16S rRNA gene fragments revealed two predominant 13C-specific bands. Sequencing of these bands indicated that carbon from 13CH4 had been assimilated by a Methylomicrobium and an uncultivated member of the Gammaproteobacteria. Cloning and sequencing of 16S rRNA genes from the heavy DNA, in addition to genes encoding particulate methane monooxygenase and methanol dehydrogenase, all linked Methylomicrobium with methane metabolism. Putative cross-feeders were affiliated with Methylophaga (Gammaproteobacteria), Hyphomicrobium (Alphaproteobacteria) and previously unrecognized methylotrophs of the Gammaproteobacteria, Alphaproteobacteria, Deferribacteres and Bacteroidetes. This first marine methane SIP study provides evidence for the presence of methylotrophs that participate in sediment food webs associated with deep-water coral reefs. [source] Exploring the diversity of bacterial communities in sediments of urban mangrove forestsFEMS MICROBIOLOGY ECOLOGY, Issue 1 2008Newton C. Marcial Gomes Abstract Municipal sewage, urban runoff and accidental oil spills are common sources of pollutants in urban mangrove forests and may have drastic effects on the microbial communities inhabiting the sediment. However, studies on microbial communities in the sediment of urban mangroves are largely lacking. In this study, we explored the diversity of bacterial communities in the sediment of three urban mangroves located in Guanabara Bay (Rio de Janeiro, Brazil). Analysis of sediment samples by means of denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments suggested that the overall bacterial diversity was not significantly affected by the different levels of hydrocarbon pollution at each sampling site. However, DGGE and sequence analyses provided evidences that each mangrove sediment displayed a specific structure bacterial community. Although primer sets for Pseudomonas, alphaproteobacterial and actinobacterial groups also amplified ribotypes belonging to taxa not intended to be enriched, sequence analyses of dominant DGGE bands revealed ribotypes related to Alteromonadales, Burkholderiales, Pseudomonadales, Rhodobacterales and Rhodocyclales. Members of these groups were often shown to be involved in aerobic or anaerobic degradation of hydrocarbon pollutants. Many of these sequences were only detected in the sampling sites with high levels of anthropogenic inputs of hydrocarbons. Many dominant DGGE ribotypes showed low levels of sequence identity to known sequences, indicating a large untapped bacterial diversity in mangrove ecosystems. [source] PCR profiling of ammonia-oxidizer communities in acidic soils subjected to nitrogen and sulphur depositionFEMS MICROBIOLOGY ECOLOGY, Issue 2 2007Christoph Stephan Schmidt Abstract Communities of ammonia-oxidizing bacteria (AOB) were characterized in two acidic soil sites experimentally subjected to varying levels of nitrogen and sulphur deposition. The sites were an acidic spruce forest soil in Deepsyke, Southern Scotland, with low background deposition, and a nitrogen-saturated upland grass heath in Pwllpeiran, North Wales. Betaproteobacterial ammonia-oxidizer 16S rRNA and ammonia monooxygenase (amoA) genes were analysed by cloning, sequencing and denaturing gradient gel electrophoresis (DGGE). DGGE profiles of amoA and 16S rRNA gene fragments from Deepsyke soil in 2002 indicated no effect of nitrogen deposition on AOB communities, which contained both Nitrosomonas europaea and Nitrosospira. In 2003, only Nitrosospira could be detected, and no amoA sequences could be retrieved. These results indicate a decrease in the relative abundance of AOB from the year 2002 to 2003 in Deepsyke soil, which may be the result of the exceptionally low rainfall in spring 2003. Nitrosospira -related sequences from Deepsyke soil grouped in all clusters, including cluster 1, which typically contains only sequences from marine environments. In Pwllpeiran soil, 16S rRNA gene libraries were dominated by nonammonia oxidizers and no amoA sequences were detectable. This indicates that autotrophic AOB play only a minor role in these soils even at high nitrogen deposition. [source] Fungal endophytes in potato roots studied by traditional isolation and cultivation-independent DNA-based methodsFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Monika Götz Abstract The composition and relative abundance of endophytic fungi in roots of field-grown transgenic T4-lysozyme producing potatoes and the parental line were assessed by classical isolation from root segments and cultivation-independent techniques to test the hypothesis that endophytic fungi are affected by T4-lysozyme. Fungi were isolated from the majority of root segments of both lines and at least 63 morphological groups were obtained with Verticillium dahliae, Cylindrocarpon destructans, Colletotrichum coccodes and Plectosporium tabacinum as the most frequently isolated species. Dominant bands in the fungal fingerprints obtained by denaturing gradient gel electrophoresis analysis of 18S rRNA gene fragments amplified from total community DNA corresponded to the electrophoretic mobility of the 18S rRNA gene fragments of the three most abundant fungal isolates, V. dahliae, C. destructans and Col. coccodes, but not to P. tabacinum. The assignment of the bands to these isolates was confirmed for V. dahliae and Col. coccodes by sequencing of clones. Verticillium dahliae was the most abundant endophytic fungus in the roots of healthy potato plants. Differences in the relative abundance of endophytic fungi colonizing the roots of T4-lysozyme producing potatoes and the parental line could be detected by both methods. [source] On the reproducibility of microcosm experiments , different community composition in parallel phototrophic biofilm microcosmsFEMS MICROBIOLOGY ECOLOGY, Issue 2 2006Guus Roeselers Abstract Phototrophic biofilms were cultivated simultaneously using the same inoculum in three identical flow-lane microcosms located in different laboratories. The growth rates of the biofilms were similar in the different microcosms, but denaturing gradient gel electrophoresis (DGGE) analysis of both 16S and 18S rRNA gene fragments showed that the communities developed differently in terms of species richness and community composition. One microcosm was dominated by Microcoleus and Phormidium species, the second microcosm was dominated by Synechocystis and Phormidium species, and the third microcosm was dominated by Microcoleus- and Planktothrix -affiliated species. No clear effect of light intensity on the cyanobacterial community composition was observed. In addition, DGGE profiles obtained from the cultivated biofilms showed a low resemblance with the profiles derived from the inoculum. These findings demonstrate that validation of reproducibility is essential for the use of microcosm systems in microbial ecology studies. [source] The influence of synthetic sheep urine on ammonia oxidizing bacterial communities in grassland soilFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Shahid Mahmood Abstract In grazed, grassland soils, sheep urine generates heterogeneity in ammonia concentrations, with potential impact on ammonia oxidizer community structure and soil N cycling. The influence of different levels of synthetic sheep urine on ammonia oxidizers was studied in grassland soil microcosms. ,Total' and active ammonia oxidizers were distinguished by comparing denaturing gradient gel electrophoresis (DGGE) profiles following PCR and RT-PCR amplification of 16S rRNA gene fragments, targeting DNA and RNA, respectively. The RNA-based approach indicated earlier, more reproducible and finer scale qualitative shifts in ammonia oxidizing communities than DNA-based analysis, but led to amplification of a small number of nonammonia oxidizer sequences. Qualitative changes in RNA-derived DGGE profiles were related to changes in nitrate accumulation. Sequence analysis of excised DGGE bands revealed that ammonia oxidizing communities in synthetic sheep urine-treated soils consisted mainly of Nitrosospira clusters 2, 3 and 4. Nitrosospira cluster 2 increased in relative abundance in microcosms treated with all levels of synthetic sheep urine. Low levels additionally led to increased relative abundance of Nitrosospira cluster 4 and medium and high levels increased relative abundance of cluster 3. Synthetic sheep urine is therefore likely to influence the spatial distribution and composition of ammonia oxidizer communities, with consequent effects on nitrate accumulation. [source] Effects of soil improvement treatments on bacterial community structure and soil processes in an upland grassland soilFEMS MICROBIOLOGY ECOLOGY, Issue 1 2003Neil D. Gray Abstract Temporal temperature gradient electrophoresis (TTGE) analysis of 16S rRNA gene fragments amplified with primers selective for eubacteria and ,-proteobacterial ammonia-oxidising bacteria (AOB) was used to analyse changes in bacterial and AOB community profiles of an upland pasture following soil improvement treatments (addition of sewage sludge and/or lime). Community structure was compared with changes in activity assessed by laboratory measurements of basal respiration and ammonia oxidation potentials, and with measurements of treatment- and time-related changes in soil characteristics. The predominant bacterial populations had a high degree of similarity under all treatment regimens, which was most pronounced early in the growing season. Most of the differences that occurred between soil samples with time could be accounted for by spatial and temporal variation; however, analysis of variance and cluster analysis of similarities between 16S rDNA TTGE profiles indicated that soil improvement treatments exerted some effect on community structure. Lime application had the greatest influence. The impact of soil improvement treatments on autotrophic ammonia oxidation was significant and sustained, especially in soils which had received sewage sludge and lime treatments in combination. However, despite obvious changes in soil characteristics, e.g. pH and soil nitrogen, increasing heterogeneity in the AOB community structure over time obscured the treatment effects observed at the beginning of the experiment. Nevertheless, time series analysis of AOB TTGE profiles indicated that the AOB community in improved soils was more dynamic than in control soils where populations were found to be relatively stable. These observations suggest that the AOB populations exhibited a degree of functional redundancy. [source] Effects of transgenic glufosinate-tolerant oilseed rape (Brassica napus) and the associated herbicide application on eubacterial and Pseudomonas communities in the rhizosphereFEMS MICROBIOLOGY ECOLOGY, Issue 3 2002Stephen Gyamfi Abstract A containment experiment was carried out in order to evaluate possible shifts in eubacterial and Pseudomonas rhizosphere community structures due to the release of genetically modified Basta-tolerant oilseed rape and the associated herbicide application. Treatments included cultivation of the transgenic plant as well as of the wild-type cultivar in combination with mechanical removal of weeds and the application of the herbicides Basta (active ingredient: glufosinate) and Butisan S (active ingredient: metazachlor). Rhizosphere soil was sampled from early and late flowering plants as well as from senescent plants. A culture-independent approach was chosen to characterize microbial communities based on denaturing gradient gel electrophoresis of 16S rRNA gene fragments amplified from rhizosphere DNA using eubacterial and Pseudomonas -specific PCR primers. Dominant pseudomonads in the rhizosphere were analyzed by sequence analysis. Whole community and Pseudomonas electrophoresis fingerprints revealed slightly altered microbial communities in the rhizosphere of transgenic plants; however, effects were minor as compared to the plant developmental stage-dependent shifts. Both herbicides caused transient changes in the eubacterial and Pseudomonas population structure, whereas differences due to the genetic modification were still detected at the senescent growth stage. The observed differences between transgenic and wild-type lines were most likely due to unintentionally modified plant characteristics such as altered root exudation. [source] Cultivation of low-temperature (15°C), anaerobic, wastewater treatment granulesLETTERS IN APPLIED MICROBIOLOGY, Issue 4 2009J. O'Reilly Abstract Aims:, Anaerobic sludge granules underpin high-rate waste-to-energy bioreactors. Granulation is a microbiological phenomenon involving the self-immobilization of several trophic groups. Low-temperature anaerobic digestion of wastes is of intense interest because of the economic advantages of unheated bioenergy production technologies. However, low-temperature granulation of anaerobic sludge has not yet been demonstrated. The aims of this study were to (i) investigate the feasibility of anaerobic sludge granulation in cold (15°C) bioreactors and (ii) observe the development of methanogenic activity and microbial community structure in developing cold granules. Methods and Results:, One mesophilic (R1; 37°C) and two low-temperature (R2 and R3, 15°C) laboratory-scale, expanded granular sludge bed bioreactors were seeded with crushed (diameter <0·4 mm) granules and were fed a glucose-based wastewater for 194 days. Bioreactor performance was assessed by chemical oxygen demand removal, biogas production, granule growth and temporal methanogenic activity. Granulation was observed in R2 and R3 (up to 33% of the sludge). Elevated hydrogenotrophic methanogenesis was observed in psychrophilically cultivated biomass, but acetoclastic methanogenic activity was also retained. Denaturing gradient gel electrophoresis of archaeal 16S rRNA gene fragments indicated that a distinct community was associated with developing and mature granules in the low-temperature (LT) bioreactors. Conclusions:, Granulation was observed at 15°C in anaerobic bioreactors and was associated with H2/CO2 -mediated methanogenesis and distinct community structure development. Significance and Impact of the Study:, Granulation underpins high-rate anaerobic waste treatment bioreactors. Most LT bioreactor trials have employed mesophilic seed sludge, and granulation <20°C was not previously documented. [source] | ||||||||||