Chemical and Microbiological in situ Characterization of Benthic Communities in Sediments with Different Contamination Levels

Lachmund, Christine; Köcher, Beate; Manz, Werner; Heininger, Peter

doi:10.1065/jss2003.09.086

Cited by 20 publications

(6 citation statements)

References 34 publications

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“…On the other hand, the conservation of a given functionality is often warranted by the flexibility of a microbial community with minority community members that may become dominant in a short period following significant perturbation (Marzorati et al 2008), thus assuring a fast recovery from a stress condition such as the presence of pollutants (Fernandez et al 2000). To ascertain how anthropogenic disturbance such as contamination input affects the microbial diversity of complex natural aquatic habitats is one of the most challenging objectives in environmental microbiology today (Lachmund et al 2003). Since the characteristics of a single species and varying consortia of microorganisms will be decisive for several other direct and indirect processes in the environment, it is equally important to investigate the functionality in relation to shifts in species composition.…”

Section: Diversity and Functionality Of Microbial Ecosystemsmentioning

confidence: 99%

Anthropogenic pollutants affect ecosystem services of freshwater sediments: the need for a “triad plus x” approach

et al. 2011

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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.

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Section: Diversity and Functionality Of Microbial Ecosystemsmentioning

confidence: 99%

Anthropogenic pollutants affect ecosystem services of freshwater sediments: the need for a “triad plus x” approach

et al. 2011

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“…Whole-cell hybridization techniques have routinely been applied for the molecular characterization of complex microbial communities for more than a decade, and they also provide quantitative data on the cellular level in terms of relative or even absolute abundances of selected populations (3). Recently, FISH analysis was also adapted to the characterization of microbial communities in lotic freshwater sediments (15,17). Moreover, identical RNA-targeting probes can be used in both formats, enabling high comparability of the two data sets.…”

Section: Vol 72 2006 Dna Microarray Analysis Of Sediment-related Bamentioning

confidence: 99%

A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities

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Lachmund

Glöckner

et al. 2006

Appl Environ Microbiol

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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 ϳ5% 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.

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“…Moreover, it was demonstrated that bacterial communities have great potential to be used as sensitive indicators of variation and contamination in coastal aquatic sediments (Lachmund et al 2003;Sun et al 2012). Although large populations of bacteria are well documented in coastal surface sediments, their biogeographical patterns under anthropogenic disturbances and environmental gradients, as well as temporal variations remain largely unexplored (Bissett et al 2006;Bertics and Ziebis 2009), especially in heterogeneous marine ecosystems such as Jiaozhou Bay (JZB).…”

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Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Liu

et al. 2014

J Soils Sediments

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Purpose Although coastal marine sediments harbor diverse bacteria with important ecological and environmental functions, a comprehensive view of their community characteristics is still lacking in typical environments along the China coast. We studied the diversity and composition of bacterial community in the sediment of Jiaozhou Bay and characterized their spatiotemporal patterns, aiming to analyze the effects of geographic heterogeneity, seasonal difference, anthropogenic activity, and eutrophication gradient on the bacterial ecology. Materials and methods Sixteen full-length bacterial 16S rRNA gene clone libraries were constructed from the sediment bacteria at four stations (A5, B2, D1, and D7) of Jiaozhou Bay over four seasons (February, May, August, and November). The bacterial diversity and community structure variation were analyzed. Results and discussion A total of 1088 16S rRNA gene sequences and 746 distinct operational taxonomic units (OTUs) (at 97 % sequence similarity level) were retrieved from the 16 clone libraries. Libraries of each sample revealed a high diversity, and a total of 17 bacterial phyla were identified.Bacteria lineages Proteobacteria (mostly γ-Proteobacteria and δ-Proteobacteria), Actinobacteria, Bacteroidetes, and Planctomycetes, which are commonly found in marine sediments, were the dominant divisions in our samples. Meanwhile, some uncommon phyla, such as Deinococcus-Thermus and Lentisphaerae, were also detected. Distinct spatial patterns and noticeable seasonal variations of bacteria community were observed, indicating that environmental heterogeneity in spatial variation other than in temporal variation may be more important in determining the bacterial communities. Most of the abundant OTUs were related to sequences retrieved from the heavy-metal-polluted environments, indicating that the Jiaozhou Bay might be influenced by pollution. Conclusions The bacterial communities in Jiaozhou Bay sediments are highly diverse. The four typical stations that we chose might experience different anthropogenic effects and eutrophication gradients, which shaped their bacterial community composition. The environment of Jiaozhou Bay may be under pressure exerted by multi-dimension anthropogenic activities. This study provided a novel insight into the bacterial community variations in Jiaozhou Bay, enriching knowledge about ecological bioindicators and mechanisms that maintain bacterial diversity and shape bacterial community composition.

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Chemical and Microbiological in situ Characterization of Benthic Communities in Sediments with Different Contamination Levels

Cited by 20 publications

References 34 publications

Anthropogenic pollutants affect ecosystem services of freshwater sediments: the need for a “triad plus x” approach

Anthropogenic pollutants affect ecosystem services of freshwater sediments: the need for a “triad plus x” approach

A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

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