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  • 1
    In: FEMS Microbiology Ecology, 2006, Vol. 56(1), pp.79-94
    Description: The microbial communities of three different habitat types and from two sediment depths in the River Elbe were investigated by fluorescence in situ hybridization at various levels of complexity. Differences in the microbial community composition of free-flowing river water, water within the hyporheic interstitial and sediment-associated bacteria were quantitatively analyzed using domain- and group-specific oligonucleotide probes. Qualitative data on the presence/absence of specific bacterial taxa were gathered using genus- and species-specific probes. The complete data set was statistically processed by univariate statistical approaches, and two-dimensional ordinations of nonmetric multidimensional scaling. The analysis showed: (1) that the resolution of microbial community structures at microenvironments, habitats and locations can be regulated by targeted application of oligonucleotides on phylogenetic levels ranging from domains to species, and (2) that an extensive qualitative presence/absence analysis of multiparallel hybridization assays enables a fine-scale apportionment of spatial differences in microbial community structures that is robust against apparent limitations of fluorescence in situ hybridization such as false positive hybridization signals or inaccessibility of in situ oligonucleotide probes. A general model for the correlation of the phylogenetic depth of focus and the relative spatial resolution of microbial communities by fluorescence in situ hybridization is presented.
    Keywords: Fluorescence Hybridization ; Microbial Communities ; Multivariate Statistics ; Rivers ; Sediments
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 2
    Language: English
    In: Water Research, 15 November 2015, Vol.85, pp.148-157
    Description: Since rivers are typically subject to rapid changes in microbiological water quality, tools are needed to allow timely water quality assessment. A promising approach is the application of predictive models. In our study, we developed multiple linear regression (MLR) models in order to predict the abundance of the fecal indicator organisms (EC), intestinal enterococci (IE) and somatic coliphages (SC) in the Lahn River, Germany. The models were developed on the basis of an extensive set of environmental parameters collected during a 12-months monitoring period. Two models were developed for each type of indicator: 1) an extended model including the maximum number of variables significantly explaining variations in indicator abundance and 2) a simplified model reduced to the three most influential explanatory variables, thus obtaining a model which is less resource-intensive with regard to required data. Both approaches have the ability to model multiple sites within one river stretch. The three most important predictive variables in the optimized models for the bacterial indicators were NH –N, turbidity and global solar irradiance, whereas chlorophyll content, discharge and NH –N were reliable model variables for somatic coliphages. Depending on indicator type, the extended mode models also included the additional variables rainfall, O content, pH and chlorophyll . The extended mode models could explain 69% (EC), 74% (IE) and 72% (SC) of the observed variance in fecal indicator concentrations. The optimized models explained the observed variance in fecal indicator concentrations to 65% (EC), 70% (IE) and 68% (SC). Site-specific efficiencies ranged up to 82% (EC) and 81% (IE, SC). Our results suggest that MLR models are a promising tool for a timely water quality assessment in the Lahn area.
    Keywords: Escherichia Coli ; Intestinal Enterococci ; Somatic Coliphages ; Bathing Water Quality ; Monitoring ; Management Tool ; Engineering
    ISSN: 0043-1354
    E-ISSN: 1879-2448
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  • 3
    Language: English
    In: PLoS ONE, 2013, Vol. 8(10)
    Description: The estuary of the River Elbe between Hamburg and the North Sea (Germany) is a sink for contaminated sediment and suspended particulate matter (SPM). One major concern is the effect of human activities on the hydrodynamics, particularlythe intensive dredging activities in this area that may result in remobilization of sediment-bound pollutants. The aim of this study was to identify pollutants contributing to the toxicological risk associated with re-suspension of sediments in the Elbe Estuary by use of an effect-directed analysis that combines chemical and biological analyses in with specific fractionation techniques. Sediments were collected from sites along the Elbe Estuary and a site from a small harbor basin of the Elbe Estuary that is known to be polluted. The sixteen priority EPA-PAHs were quantified in organic extracts of sediments. In addition, dioxin equivalents of sediments were investigated by use of the 7-ethoxyresorufin O-deethylase assay with RTL-W1 cells and the Ah receptor-mediated luciferase transactivation assay with H4IIE-luc cells. Quantification of the 16 priorityPAHs revealed that sediments were moderately contaminated at all of the sites in the Elbe River Estuary (,0.02–0.906 mg/gdw). Sediments contained relatively small concentrations of dioxin equivalents (Bio-TEQ) with concentrations ranging from15.5 to 322 pg/g dw, which were significantly correlated with dioxin equivalents calculated based on toxicity referencevalues and concentrations of PAH. The concentration of Bio-TEQ at the reference site exceeded 200,000 pg/g dw. In apotency balance the 16 PAHs explained between 47 and 118% of the Bio-TEQ in the luciferase assay, which can be explained by the constant input of PAHs bound to SPM from the upper course of the Elbe River into its estuary. Successful identification of a significant portion of dioxin-like activity to priority PAHs in complex environmental samples such assediments has rarely been reported.
    Keywords: Natural Sciences ; Earth And Related Environmental Sciences ; Environmental Sciences ; Naturvetenskap ; Geovetenskap Och Miljövetenskap ; Miljövetenskap ; Enviromental Science ; Miljövetenskap
    ISSN: 1932-6203
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  • 4
    Language: English
    In: Journal of Soils and Sediments, 2011, Vol.11(6), pp.1099-1114
    Description: Byline: Sabine Ulrike Gerbersdorf (1), Henner Hollert (2), Markus Brinkmann (2), Silke Wieprecht (1), Holger Schuttrumpf (3), Werner Manz (4) Keywords: Biofilm; Freshwater; Interdisciplinary approach; Management of sediments; Pollutants; Risk assessment Abstract: Purpose Freshwater sediments and their attached microbial communities (biofilms) are essential features of rivers and lakes, providing valuable ecosystem services such as nutrient recycling or self-purification which extend beyond the aquatic environment. Anthropogenic pollutants, whether from the industrial era or as a result of our contemporary lifestyles, can negatively affect these functions with hitherto unknown consequences on ecology, the economy and human health. Thus far, the singular view of the involved disciplines such as ecotoxicology, environmental microbiology, hydrology and geomorphology has prevented a deeper understanding of this emerging issue. Main features This paper discusses briefly the progressions and the state-of-the-art methods within the disciplines of concern related to contaminated sediments, ranging from ecotoxicological test systems, microbiological/molecular approaches to unravel changes of microbial ecosystems, up to the modelling of sediment transport and sorption/desorption of associated pollutants. The first bilateral research efforts on contaminated sediments include efforts to assess ecotoxicological sediment risk including sediment mobility (i.e. ecotoxicology and engineering), enhance bioremediation potential (i.e. microbiology and ecotoxicology) or to understand biostabilisation processes of sediments by microbial assemblages (i.e. microbiology and engineering). Conclusions and perspectives In freshwater habitats, acute, chronic and mechanism-specific toxic effects on organisms, shifts in composition, structure and functionality of benthic microbial communities, as well as the obstruction of important ecosystem services by continuously discharged and long-deposited pollutants, should be related to the in situ sediment dynamics. To achieve an improved understanding of the ecology of freshwater sediments and the impairment of their important ecosystem functions by human-derived pollutants, we suggest a "triad plus x" approach combining advanced methods of ecotoxicology, environmental microbiology and engineering science. Author Affiliation: (1) Department of Hydraulic Engineering and Water Resources Management, Institute of Hydraulic Engineering, University Stuttgart, Pfaffenwaldring 61, 70569, Stuttgart, Germany (2) Department of Ecosystem Analysis, Institute for Environmental Research, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany (3) Institute of Hydraulic Engineering and Water Resources Management, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, 52056, Aachen, Germany (4) Institute for Integrated Natural Sciences, University Koblenz--Landau, Universitatsstrasse 1, 56070, Koblenz, Germany Article History: Registration Date: 25/04/2011 Received Date: 20/11/2010 Accepted Date: 24/04/2011 Online Date: 11/05/2011 Article note: Responsible editor: Ian G. Droppo
    Keywords: Biofilm ; Freshwater ; Interdisciplinary approach ; Management of sediments ; Pollutants ; Risk assessment
    ISSN: 1439-0108
    E-ISSN: 1614-7480
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  • 5
    Language: English
    In: Research and Reports in Biology, 2018, Vol.9, p.1(16)
    Description: Biofilms constitute an important issue in microbial ecology, due to their high ecological and economic relevance, but the impact of abiotic conditions and microbial key players on the development and functionality of a natural biofilm is still little understood. This study investigated the effects of light intensity (LI) and bed shear stress (BSS) and the role of dominant microbes during the formation of natural biofilms and particularly the process microbial biostabilization. A comprehensive analysis of microbial biomass, extracellular polymeric substances produced, and the identification of dominant bacterial and algal species was correlated with assessment of biofilm adhesiveness/stability. LI and BSS impacted the biofilms in very different ways: biofilm adhesiveness significantly increased with LI and decreased with BSS. Moreover, microbial biomass and the functional organization of the bacterial community increased with LI, while the dynamics in the bacterial community increased with BSS. Most stable biofilms were dominated by sessile diatoms like Achnanthidium minutissimum or Fragilaria pararumpens and bacteria with either filamentous morphology, such as Pseudanabaena biceps, or a potential high capacity for extracellular polymeric-substance production, such as Rubrivivax gelatinosus. In contrast, microbes with high motility, such as Nitzschia fonticola, Pseudomonas fluorescens, and Caulobacter vibrioides, dominated the least adhesive biofilms. Their movement and potential antibiotic production could have had a disruptive impact on the biofilm matrix, which decreased its stability. This is the first study to unveil the link between abiotic conditions and resulting shifts in key microbial players to impact the ecosystem-service microbial biostabilization. Keywords: microbial biostabilization, natural biofilms, abiotic factors, microbial community, mesocosm
    Keywords: Ecosystem Components – Analysis
    ISSN: 1179-7274
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  • 6
    In: Applied and Environmental Microbiology, 2008, Vol. 74(20), p.6427
    Description: New rRNA-targeting oligonucleotide probes permitted the fluorescence in situ hybridization (FISH) identification of freshwater fungi in an Austrian second-order alpine stream. Based on computer-assisted comparative sequence analysis, nine taxon-specific probes were designed and evaluated by whole-fungus hybridizations. Oligonucleotide probe MY1574, specific for a wide range of Eumycota, and the genus (Tetracladium)-specific probe TCLAD1395, as well as the species-specific probes ALacumi1698 (Alatospora acuminata), TRIang322 (Tricladium angulatum), and Alongi340 (Anguillospora longissima), are targeted against 18S rRNA, whereas probes TmarchB10, TmarchC1_1, TmarchC1_2, and AlongiB16 are targeted against the 28S rRNA of Tetracladium marchalianum and Anguillospora longissima, respectively. After 2 weeks and 3 months of exposure of polyethylene slides in the stream, attached germinating conidia and growing hyphae of freshwater fungi were accessible for FISH. Growing hyphae and germinating conidia on leaves and in membrane cages were also visualized by the new FISH probes.
    Keywords: Fresh Water -- Microbiology ; Fungi -- Isolation & Purification ; In Situ Hybridization, Fluorescence -- Methods ; Oligonucleotide Probes -- Genetics;
    ISSN: 0099-2240
    ISSN: 00992240
    E-ISSN: 10985336
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  • 7
    In: Applied and Environmental Microbiology, 2006, Vol. 72(7), p.4829
    Description: A DNA microarray platform for the characterization of bacterial communities in freshwater sediments based on a heterogeneous set of 70 16S rRNA-targeted oligonucleotide probes and directly labeled environmental RNA was developed and evaluated. Application of a simple protocol for the efficient background blocking of aminosilane-coated slides resulted in an improved signal-to-noise ratio and a detection limit of 10 ng for particular 16S rRNA targets. An initial specificity test of the system using RNA from pure cultures of different phylogenetic lineages showed a fraction of false-positive signals of approximately 5% after protocol optimization and a marginal loss of correct positive signals. Subsequent microarray analysis of sediment-related community RNA from four different German river sites suggested low diversity for the groups targeted but indicated distinct differences in community composition. The results were supported by parallel fluorescence in situ hybridization in combination with sensitive catalyzed reporter deposition (CARD-FISH). In comparisons of the data of different sampling sites, specific detection of populations with relative cellular abundances down to 2% as well as a correlation of microarray signal intensities and population size is suggested. Our results demonstrate that DNA microarray technology allows for the fast and efficient precharacterization of complex bacterial communities by the use of standard single-cell hybridization probes and the direct detection of environmental rRNA, also in methodological challenging habitats such as heterogeneous lotic freshwater sediments.
    Keywords: Engineering ; Biology ; Economics;
    ISSN: 0099-2240
    ISSN: 00992240
    E-ISSN: 10985336
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  • 8
    In: Environmental Science: Nano, 2016, Vol.3(2), pp.418-433
    Description: Understanding of the interplay of generally known colloidal transformations under conditions of test media (TM) used during cultivation of organisms and biological effect (=ecotoxicological) studies is still limited, although this knowledge is required for an adequate interpretation of test outcomes and for a comparison among different studies. In this context, we investigated the aggregation and dissolution dynamics of citrate-stabilized silver nanoparticles (Ag NPs) by varying the composition of three TM (ASTM, SAM-5S, and R2A, used during bioassays with Daphnia magna , Gammarus fossarum , and bacterial biofilms, respectively) in the presence and absence of two types of natural organic matter (NOM), namely, Suwanee River humic acid (SRHA) and seaweed extract (SW). Each original test medium induced reaction-limited aggregation of Ag NPs, and aggregation increased from R2A to SAM-5S and ASTM. In addition to the differences in aggregation dynamics, the concentration and speciation of Ag( i ) differed between the three TM, whereby SAM-5S and ASTM are comparable with respect to the nature of the aggregation process but clearly differ from the R2A medium. Furthermore, Cl , mainly present in SAM-5S, induced NP stabilization. The release of silver ions from Ag NPs was controlled by the presence of NOM and organic constituents of TM and by interactions with Cl and Br . The degree of aggregation, formation of interparticle cationNOM bridges or stabilization was larger for Ca 2+ than for Mg 2+ due to the stronger ability of Ca 2+ to interact with citrate or NOM compared to Mg 2+ . These observations and the dependence of aggregation rates on the particle concentration renders the interpretation of doseresponse relationships challenging, but they may open perspectives for targeted ecotoxicological testing by modifications of TM composition.
    Keywords: Bacteria ; Media ; Stabilization ; Concentration (Composition) ; Silver ; Nanoparticles ; Dynamics ; Agglomeration ; Chemical and Electrochemical Properties (MD) ; Chemical and Electrochemical Properties (Ep) ; Chemical and Electrochemical Properties (Ed) ; Chemical and Electrochemical Properties (EC);
    ISSN: 2051-8153
    E-ISSN: 2051-8161
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  • 9
    Language: English
    In: Diseases of Aquatic Organisms, 2010, Vol. 23, pp. 235-248
    Description: Despite intensive efforts and tightened guidelines for improvement of water quality over the last 2 decades, declines of fish populations have been reported for several rivers around the world. The present study forms part of a comprehensive weight-of-evidence approach, which aims to identify potential causes for the decline in fish catches observed in the Upper Danube River. The major focus of the present study is the investigation of the health status of wild barbel Barbus barbus L. collected from 3 locations along the Danube River, which experienced different levels of contamination. Whereas the comparison of the condition factor (CF) of field fish with that of control fish revealed no differences, ultrastructural investigations indicated severe disturbance of hepatic cell metabolism in field fish from the more contaminated sites Rottenacker and Ehingen, compared to both control fish and field fish from the less contaminated site Riedlingen. The ultrastructural analysis provided information about reactions of e.g. the rough endoplasmic reticulum, peroxisomes, andmitochondria, indicating an impaired health status of barbel at the sampling sites Rottenacker and Ehingen. Even though a straightforward cause-effect relationship between sediment contamination and ultrastructural alterations could not be established, based on a meta-analysis and toxicity assays it may be suggested that sediment-bound xenobiotics at least partly account for the hepatocellular changes. A relationship between impaired fish health status and the decline of fish catches along the Upper Danube River cannot be excluded.
    Keywords: Danube River ; Fish ; Population Decline ; Liver Ultrastructure ; Barbus Barbus ; Condition Factor ; Sediment ; Natural Sciences ; Earth And Related Environmental Sciences ; Environmental Sciences ; Naturvetenskap ; Geovetenskap Och Miljövetenskap ; Miljövetenskap ; Enviromental Science ; Miljövetenskap
    ISSN: 0177-5103
    E-ISSN: 16161580
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  • 10
    Language: English
    In: Reproductive Toxicology, April 2012, Vol.33(2), pp.245-253
    Description: ► This study analyzes the usability of transcriptomics for the characterization of sediment extract toxicity. ► Altered gene expression was compared to data from established bioassays as well as to chemical analysis. ► Gene expression profiling could be documented as a useful tool for the investigation of sediment extracts. ► Only a limited number of altered gene expression could be explained by analytical chemistry or biological effects. The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This proof-of-concept study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in sediment extracts. For this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Mechanism-specific biotests indicated a defined hazard potential of the sediment extracts, and microarray analysis revealed several classes of significantly regulated genes which could be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism.
    Keywords: Microarray ; Transcriptomics ; Zebrafish ; Sediment Extract ; Comet Assay ; Erod Assay ; Ames Test ; Neutral Red Assay ; Chemistry ; Anatomy & Physiology ; Public Health
    ISSN: 0890-6238
    E-ISSN: 1873-1708
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