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  • Sediments
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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: PLoS ONE, 02 November 2010, Vol.5(11), pp.1-12
    Description: It is recognized that microorganisms inhabiting natural sediments significantly mediate the erosive response of the bed (‘‘ecosystem engineers'') through the secretion of naturally adhesive organic material (EPS: extracellular polymeric substances). However, little is known about the individual...
    Keywords: Life Sciences ; Ecology, Environment ; Life Sciences ; Microbiology and Parasitology ; Sciences (General)
    ISSN: 1932-6203
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: PLoS ONE, 01 January 2018, Vol.13(6), p.e0199132
    Description: The application of engineered silver nanoparticles (AgNPs) in a considerable amount of registered commercial products inevitably will result in the continuous release of AgNPs into the natural aquatic environment. Therefore, native biofilms,...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 4
    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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  • 5
    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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  • 6
    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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  • 7
    Language: English
    In: Ecological indicators, 2012, Vol.19, pp.118-129
    Description: Indices to assess the ecological status of water bodies according to the European Water Framework Directive (WFD) frequently produce widely differing results when applied to estuarine systems. Although several ecological indices have been employed to coastal environments and in estuaries in particular, there is still a lack of knowledge about their suitability for assessing the ecological status of heavily modified water bodies. Thus, we evaluated the performances of indices and fauna parameters (AMBI, M-AMBI, BOPA, BO2A, W-value, Shannon diversity, species richness, abundance) that have been discussed in the WFD context using data on invertebrates dwelling in two typical morphological units: the navigation channel and the river bank habitats of Elbe estuary (Germany). In addition, we tested their ability to identify several environmental factors (grain size distribution and chemical sediment contamination). All indices were able to detect major changes in macrofauna composition along the estuarine salinity gradient and were able to differentiate between navigation channel and shallow bank habitats. A strong significant correlation was found with most indices with the exceptions of the W-value and the BOPA with mean grain size. Almost all indices signaled poor ecological quality in the coarser fairway sediments against the finer sublitoral bank sediments. However, AMBI and BOPA showed the opposite: both indicators classified the invertebrate assemblages from the navigation channel better compare than the shallower habitats. The correlation of ecological indices and parameters with sediment contaminants and the toxicity of the sediment calculated as toxic units showed a diverse picture: all indices, except species richness and the BOPA, had a certain significant correlation with several individual sediment pollutants, however, only one index, the W-value, was correlated significant with the majority of chemical pollutants (Pb, Cd, Cu, Ni, Hg, Zn, β-HCH, pp′-DDD, and TBT) and the toxic units. Our results show clearly that ecological quality classification of heavily modified estuaries depends strongly on both the index and the habitat. Thus, we conclude that no index should be used on its own to estimate the ecological quality of estuaries. Further investigations and the improvement or development of such indices should place emphasis on their independence from the grain size spectrum of the sediments and on their good correlation with its pollution status. ; p. 118-129.
    Keywords: Zinc ; Environmental Factors ; Habitats ; Hch (Pesticide) ; Copper ; Fauna ; Pollutants ; Surface Water ; Lead ; Salinity ; Invertebrates ; Sediment Contamination ; Estuaries ; Toxicity ; Sediments ; Cadmium ; Nickel ; Species Diversity ; Mercury
    ISSN: 1470-160X
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 8
    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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  • 9
    Language: English
    In: Analytical and Bioanalytical Chemistry, 2008, Vol.390(8), pp.2009-2019
    Description: This study is a consequence of a distinct fish decline in the Danube river since the beginning of the 1990s. In contrast to the decline of fish population, former studies have repeatedly documented that the water quality along the Danube river is improving. However, the conclusion of a pilot study in 2002 was that a high hazard potential is associated with local sediments. The present study documents that sediment samples from the Danube river showed comparatively high aryl hydrocarbon receptor mediated activity in biotests, using the cell lines GPC.2D.Luc, H4IIE (DR-CALUX®) and RTL-W1. The combination of chemical analysis, fractionation techniques and different in vitro tests revealed that priority pollutants could not explain the main induction, even though the concentrations of priority polycyclic aromatic hydrocarbons (PAHs) were very high (maximum in the tributary Schwarzach, sum of 16 EPA PAHs 26 μg/g). In conclusion, this investigation shows that nonpriority pollutants mainly mediate the high induction rates. Nevertheless, owing to the effects of PAHs towards fish and the connection between dioxin-like activity and carcinogenicity, the link between contamination and the fish population decline cannot be ruled out.
    Keywords: Danube ; Fish decline ; Dioxin-like activity ; Aryl hydrocarbon receptor agonists ; Weight of evidence
    ISSN: 1618-2642
    E-ISSN: 1618-2650
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  • 10
    In: FEMS Microbiology Ecology, 2008, Vol. 66(2), pp.282-294
    Description: The secretion of extracellular polymeric substances (EPS) by bacteria has been recognized as important across a wide range of scientific disciplines, but in natural sediments, EPS production by microalgae as a mechanism of sediment stabilization has received much more attention than bacterial products. In the present study, the stabilization potential of a natural benthic bacterial assemblage was tested in cultures growing on noncohesive glass beads. The surface erosion resistance as determined by a cohesive strength meter was significantly enhanced over time compared with controls. Nutrient enrichment of the bacterial assemblages by a general broth (bacteria+) resulted in enhanced stabilization (× 3.6) compared with nutrient-depleted (bacteria) assemblages (× 1.8). This correlated with higher bacterial biomass and EPS concentrations in enriched cultures. Substratum stability was closely related to bacterial cell numbers ( R 2 =0.75/0.78) and EPS protein concentrations ( R 2 =0.96/0.53) (for bacteria/bacteria+ treatments, respectively), but not to EPS carbohydrates. This study implies a greater significance of extracellular proteins in substratum cohesion within the EPS complex than recognized previously. The data show both the importance of bacterial assemblages for microbial sediment stabilization and that a change in abiotic conditions can significantly affect sediment stabilization.
    Keywords: Extracellular Polymeric Substances ; Bacterial Engineering ; Sediment Stability ; Sediment Erosion
    ISSN: 01686496
    E-ISSN: 1574-6941
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