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PubMed2001

Bacteria in gel probes: comparison of the activity of immobilized sulfate-reducing bacteria with in situ sulfate reduction in a wetland sediment.

A novel method was used to examine the microbial ecology of iron-rich wetland sediments receiving neutral-pH coal mine drainage. Gel probes inserted into the sediments allowed analysis of the distribution and activity of bacterial sulfate reduction (BSR). A mixed population of sulfate-reducing bacteria enriched from anoxic wetland sediments was immobilized in low temperature-gelling agarose held in grooved rods or probes. The probes were inserted vertically into sediments and were allowed to incubate in situ for 48 h. After their retrieval, the gels were sectioned and analyzed for residual BSR activity and were compared to in situ BSR rates and chemical porewater profiles. The depth distribution of residual BSR activity in the immobilized cell gel probes differed significantly from the BSR measured in situ. Approximately 51% of the total integrated residual sulfate reduction activity measured in the gel probes occurred between 0 and 7 cm of the upper 20 cm of sediment. In contrast, ca. 99% of the integrated in situ BSR occurred between 7- and 20-cm depth, and only 1% of the total integrated rate occurred between 0- and 7-cm depth. Lactate-enriched bacteria immobilized in the gel may have been atypical of the majority of sulfate-reducing bacteria in the sediment. Agarose-immobilized sulfate-reducing bacteria might also be able to proliferate in the otherwise inhospitable zone of iron reduction, where sulfate and labile carbon compounds for which they are usually outcompeted can diffuse freely into the gel matrix. Gel probes containing particulate iron monosulfide (FeS) indicated that FeS remained stable in sediments at depths greater than 2 to 3 cm below the sediment-water interface, consistent with the shallow penetration of oxygen into surface sediments.

Acrylic Resins↗

PubMed2003

Optimization of direct cell counting in sediment.

This study reports a method for optimizing direct counts of bacteria in sediment, designed to reduce the masking by sediment particles. The protocol was designed to determine appropriate dilution factors by incorporating counting statistics and was used to measure depth-associated changes in microbial abundance in metal-impacted freshwater sediments. We demonstrated a direct method to determine appropriate sample dilution for accurate counting by adding a known amount of cells to the sediment. For accurate counting in our sediment samples, we determined that the average number of bacteria per microscope ocular field must be between 8.5 and 10. This is well below the 30 bacteria/field previously suggested for accurate counting. These results indicate that an optimal dilution rate must be determined before accurate direct counts in sediment can be achieved.

Bacteria↗

PubMed2001

Particle-scale investigation of PAH desorption kinetics and thermodynamics from sediment.

Dredged sediment from Milwaukee Harbor showed two primary classes of particles in the <2 mm size range: a lighter-density coal- and wood-derived fraction with 62% of total PAHs and a heavier-density sand, silt, and clay fraction containing the remaining 38% of the PAHs. Room-temperature PAH desorption kinetic studies on separated sediment fractions revealed slow desorption rates for the coal-derived particles and fast desorption rates for the clay/silt particles. The effect of temperature on PAH release was measured by thermal program desorption mass spectrometry to investigate the desorption activation energies for PAHs on the different sediment particles. Three activated diffusion-based models and an activated first-order rate model were used to describe the thermal desorption of PAHs for four molecular weight classes. PAH binding with the coal-derived particles was associated with high activation energies, typically in the range of 115-139 kJ/mol. PAHs bound to the clay/silt material had much lower activation energy, i.e., in the range of 37-41 kJ/ mol for molecular weight 202. Among the desorption models tested, a spherical diffusion model with PAHs located like a rind on the outer 1-3 microm region best described the PAH thermal desorption response for coal-derived particles. This internal PAH distribution pattern on coalderived particles is based on prior direct measurement of PAH locations at the subparticle scale. These studies reveal that heterogeneous particle types in sediment exhibit much different amounts and binding of PAHs. PAHs associated with coal-derived particles aged over several decades in the field appear to be far from reaching an equilibrium sorption state due to the extremely slow diffusivities through the polymer-like coal matrix. These results provide an improved mechanistic perspective for the understanding of PAH mobility and bioavailability in sediments.

Adsorption↗

PubMed2001

Testing bioassessment metrics: macroinvertebrate, sculpin, and salmonid responses to stream habitat, sediment, and metals.

The purpose of this article is to report on the testing of responses of multimetric macroinvertebrate and habitat indices to common disturbances to streams: stream habitat alteration, excessive sediment, and elevated metals concentrations. Seven macroinvertebrate community metrics were combined into a macroinvertebrate biotic index (MBI), and 11 channel morphology, riparian, and substrate features were combined into a habitat index. Indices were evaluated by comparing the habitat results to fish population surveys and comparing the macroinvertebrate results to habitat ratings, percent fine sediments measured by Wolman pebble counts, and copper concentrations. Macroinvertebrate scores decreased with increasing percentages of fine sediments measured either across the bankfull or instream channel widths. Macroinvertebrate scores decreased with increasing copper. One metric, richness of Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa, was more responsive to both copper and sediment than was the multimetric MBI. Habitat scores corresponded well with the age class structure of salmonids, but not with that of benthic sculpins. Both salmonid and sculpin age classes declined with increasing percentages of fine sediments. The decline was graded with the sculpin age classes, whether fine sediments were measured across the instream or bankfull channel, whereas salmonids consistently responded only to the instream fine sediments.

Animals↗

PubMed1999

Removal of mercury from mercury-contaminated sediments using a combined method of chemical leaching and volatilization of mercury by bacteria.

A method for the removal of mercury sulfide from mercury-contaminated sediments was developed, which consists of chemical leaching and volatilization of mercury by bacteria. More than 85% of the mercury in sediment containing 0.11-37.4 mg/kg of mercury was efficiently extracted with 3 M HCl and 74 mM FeCl3. Subsequent volatilization by bacteria resulted in the removal of 62.9-75.1% of mercury from mercury-contaminated Minamata Bay sediments. Methylmercury was also eliminated from soil at a high efficiency. Thus, this combined method of chemical and microbial treatments could be used for efficient removal of both organic and inorganic mercurials from natural sediments.

Bacteria↗

PubMed2003

Characterisation of trace elements and methylmercury in an estuarine sediment reference material, IAEA-405.

An estuarine sediment sample, IAEA-405, was recently characterised for trace elements and methylmercury (MeHg) for ultimate use as a marine reference material. The reference values were calculated using data sets from 120 laboratories that participated in a world-wide intercomparison exercise. The data evaluation is highlighted, and includes comparisons of different analytical methods, as well as the distribution of data. Overall laboratory performance for this exercise was encouraging: 86 laboratories (72%) reported data with <25% outliers. There was sufficient acceptable data to establish recommended values for 17 elements and information values for a further 15 elements. In addition, a recommended value was established for methylmercury. The estuarine sediment sample, IAEA-405, can be used as a reference material for quality control in the determination of trace elements and methylmercury in moderately polluted sediments.

Environmental Monitoring↗

PubMed2005

Behavior of di(2-ethylhexyl) phthalate discharged from domestic waste water into aquatic environment.

The behavior of di(2-ethylhexyl) phthalate (DEHP) discharged from domestic waste water into river water, sediment and submerged aquatic vegetation was investigated. The concentrations of DEHP were found to be between 8-25 microg L(-1) in river water, 1,000-2,000 microg kg(-1) in sediment and less than 20-2,000 microg kg(-1) in submerged aquatic vegetation. The experiments performed in laboratory were on the biodegradation of DEHP in water and sediment, and also adsorption equilibrium of DEHP between water and sediment. The results obtained from the investigations made it clear that the high enrichment of DEHP from water to sediment was caused from not only its high adsorptive potential but also slow degradation in sediment.

Adsorption↗

PubMed2001

Origin and distribution of sulphate in surface waters of the Mansfeld mining district (Central Germany)--a sulphur isotope study.

In the Mansfeld region (Central Germany) copper mining contributed to an enormous pollution of the environment. Metal- and sulphate-bearing sediments and leachates emerge from the former copper smelters and mining waste heaps, spread along local rivers and finally reach the Saale river. A sulphur isotope study on water and stream sediments was performed along the River "Böse Sieben" and from its tributaries to determine the different sulphur sources. Four major sulphur sources exist in the area: metal sulphide mineralisations (Kupferschiefer), met alliferous sulphidic flue dust, slag, and anhydrite and gypsum of Permian and Triassic age. We obtained delta34S(SO4)-values in water samples varying from +4 per thousand to -18 per thousand CDT, clearly reflecting the input of sulphate from different sources. Sulphate from the oxidation of sulphidic mining residues is restricted to the mining area and cannot be traced for more than 5 km downstream. The major source for sulphate is the dissolution of gypsum and anhydrite. The sulphur isotope composition in dissolved and sedimentary adsorbed sulphate differs only slightly from each other. Microbial dissimilatory sulphate reduction can not be excluded in the shallow sediment layers.

Adsorption↗

PubMed2005

A new and fast extraction method for the determination of priority phenols from marine sediments by liquid chromatography.

A new and fast method for the determination of priority phenols in marine sediment samples by high-performance liquid chromatography using microwave-assisted micellar extraction is optimized. This study is carried out using the nonionic surfactants polyoxyethylene 9 lauryl ether (polidocanol) and genapol X-080 as extractants. Parameters studied include surfactant concentration, solution pH, extraction time, and power. Once the method is optimized, it is applied to different spiked marine sediments from of the Canary Islands coastlines (Spain). The results obtained indicate that a power irradiation of 500 W for 2 min achieved the best extraction efficiency (approximately 100% recovery) and less than 10% relative standard deviation. Detection limits are obtained in the 2-20 microg/g range for the phenols studied. Finally, the proposed method provides a simple, fast, and organic solvent-free procedure to analyze phenols from marine sediment samples.

Chromatography, Liquid↗

PubMed2006

Quantification of microbial communities in near-surface and deeply buried marine sediments on the Peru continental margin using real-time PCR.

Deeply buried marine sediments harbour a large fraction of all prokaryotes on Earth but it is still unknown which phylogenetic and physiological microbial groups dominate the deep biosphere. In this study real-time PCR allowed a comparative quantitative microbial community analysis in near-surface and deeply buried marine sediments from the Peru continental margin. The 16S rRNA gene copy numbers of prokaryotes and Bacteria were almost identical with a maximum of 10(8)-10(10) copies cm(-3) in the near-surface sediments. Archaea exhibited one to three orders of magnitude lower 16S rRNA gene copy numbers. The 18S rRNA gene of Eukarya was always at least three orders of magnitude less abundant than the 16S rRNA gene of prokaryotes. The 16S rRNA gene of the Fe(III)- and Mn(IV)-reducing bacterial family Geobacteraceae and the dissimilatory (bi)sulfite reductase gene (dsrA) of sulfate-reducing prokaryotes were abundant with 10(6)-10(8) copies cm(-3) in near-surface sediments but showed lower numbers and an irregular distribution in the deep sediments. The copy numbers of all genes decreased with sediment depth exponentially. The depth gradients were steeper for the gene copy numbers than for numbers of total prokaryotes (acridine orange direct counts), which reflects the ongoing degradation of the high-molecular-weight DNA with sediment age and depth. The occurrence of eukaryotic DNA also suggests DNA preservation in the deeply buried sediments.

Archaea↗

PubMed2006

Synoptic determination of living/dead and active/dormant bacterial fractions in marine sediments.

The most widely used methods for the estimation of the living/dead fractions of bacterial cells involve specific stains that are able to reveal membrane integrity. Here, we have compared two different probes (propidium iodide and ethidium homodimer-2) that have different molecular weights and steric hindrance effects. We have also combined this method with the staining/destaining procedure that is currently used in the identification of potentially active cells. The procedure for marine sediments described here allows the synoptic (i.e. from the same filter) identification of: (i) the number of living bacteria; (ii) the number of active vs. dormant cells within this living fraction; (iii) the bacterial fraction with an intact nucleoid region without membrane integrity; and (iv) dead cells (devoid of the nucleoid region and without membrane integrity). Our results demonstrate that the concentration of propidium is crucial for the correct estimation of the dead bacterial fraction, ethidium homodimer-2 allows efficient and accurate estimates that are independent of the concentrations used and the sample storage. The active bacterial fraction represented c. 40% of the total bacterial abundance, the inactive/dormant fraction c. 30%, and the dead fraction was, on average, c. 30%. This method allows the processing of a large number of samples with high precision and at relatively low cost, and thus it provides additional synoptic insights into the metabolic state of bacteria in marine sediments.

Bacteria↗

PubMed2006

Molecular evidence for the broad distribution of anaerobic ammonium-oxidizing bacteria in freshwater and marine sediments.

Previously available primer sets for detecting anaerobic ammonium-oxidizing (anammox) bacteria are inefficient, resulting in a very limited database of such sequences, which limits knowledge of their ecology. To overcome this limitation, we designed a new primer set that was 100% specific in the recovery of approximately 700-bp 16S rRNA gene sequences with >96% homology to the "Candidatus Scalindua" group of anammox bacteria, and we detected this group at all sites studied, including a variety of freshwater and marine sediments and permafrost soil. A second primer set was designed that exhibited greater efficiency than previous primers in recovering full-length (1,380-bp) sequences related to "Ca. Scalindua," "Candidatus Brocadia," and "Candidatus Kuenenia." This study provides evidence for the widespread distribution of anammox bacteria in that it detected closely related anammox 16S rRNA gene sequences in 11 geographically and biogeochemically diverse freshwater and marine sediments.

Bacteria, Anaerobic↗

PubMed2006

A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities.

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.

Bacteria↗

PubMed1999

Acetogenic and sulfate-reducing bacteria inhabiting the rhizoplane and deep cortex cells of the sea grass Halodule wrightii.

Recent declines in sea grass distribution underscore the importance of understanding microbial community structure-function relationships in sea grass rhizospheres that might affect the viability of these plants. Phospholipid fatty acid analyses showed that sulfate-reducing bacteria and clostridia were enriched in sediments colonized by the sea grasses Halodule wrightii and Thalassia testudinum compared to an adjacent unvegetated sediment. Most-probable-number analyses found that in contrast to butyrate-producing clostridia, acetogens and acetate-utilizing sulfate reducers were enriched by an order of magnitude in rhizosphere sediments. Although sea grass roots are oxygenated in the daytime, colorimetric root incubation studies demonstrated that acetogenic O-demethylation and sulfidogenic iron precipitation activities were tightly associated with washed, sediment-free H. wrightii roots. This suggests that the associated anaerobes are able to tolerate exposure to oxygen. To localize and quantify the anaerobic microbial colonization, root thin sections were hybridized with newly developed (33)P-labeled probes that targeted (i) low-G+C-content gram-positive bacteria, (ii) cluster I species of clostridia, (iii) species of Acetobacterium, and (iv) species of Desulfovibrio. Microautoradiography revealed intercellular colonization of the roots by Acetobacterium and Desulfovibrio species. Acetogenic bacteria occurred mostly in the rhizoplane and outermost cortex cell layers, and high numbers of sulfate reducers were detected on all epidermal cells and inward, colonizing some 60% of the deepest cortex cells. Approximately 30% of epidermal cells were colonized by bacteria that hybridized with an archaeal probe, strongly suggesting the presence of methanogens. Obligate anaerobes within the roots might contribute to the vitality of sea grasses and other aquatic plants and to the biogeochemistry of the surrounding sediment.

Acetates↗

PubMed2002

Impact of irradiation and polycyclic aromatic hydrocarbon spiking on microbial populations in marine sediment for future aging and biodegradability studies.

Experiments were carried out to develop methods to generate well-characterized, polycyclic aromatic hydrocarbon (PAH)-spiked, aged but minimally altered sediments for fate, biodegradation, and bioavailability experiments. Changes in indigenous bacterial populations were monitored in mesocosms constructed of relatively clean San Diego Bay sediments, with and without exposure to gamma radiation, and then spiked with five different PAHs and hexadecane. While phenanthrene and chrysene degraders were present in the unspiked sediments and increased during handling, PAH spiking of nonirradiated sediments led to dramatic increases in their numbers. Phenotypic characterization of isolates able to grow on phenanthrene or chrysene placed them in several genera of marine bacteria: Vibrio, Marinobacter or Cycloclasticus, Pseudoalteromonas, Marinomonas, and HALOMONAS: This is the first time that marine PAH degraders have been identified as the latter two genera, expanding the diversity of marine bacteria with this ability. Even at the highest irradiation dose (10 megarads), heterotrophs and endospore formers reappeared within weeks. However, while bacteria from the unirradiated sediments had the capacity to both grow on and mineralize 14C-labeled phenanthrene and chrysene, irradiation prevented the reappearance of PAH degraders for up to 4 months, allowing spikes to age onto the sediments, which can be used to model biodegradation in marine sediments.

Biodegradation, Environmental↗

PubMed2003

Speciation of heavy metals in recent sediments of three coastal ecosystems in the Gulf of Cádiz, southwest Iberian Peninsula.

A live-step sequential extraction technique was used to determine the partitioning of Cr, Mn, Fe, Cu, Zn, Cd, and Pb among the operative sedimentary phases (exchangeable ions, carbonates, manganese and iron oxides, sulfides and organic matter. and residual minerals) in coastal sediment from three locations in the southwest Iberian Peninsula. Two sites are located close to industrial areas, the salt marshes of the Odiel River and Bay of Cádiz, and one in a nonindustrial area, the Barbate River salt marshes. The Odiel River salt marshes also receive the drainage from mining activities in the Huelva region. In the sediments from the Bay of Cádiz and Barbate River salt marshes, Cr, Cu, Fe, and Zn were extracted from the residual fraction at percentages higher than 60%. In the sediments from the Odiel River salt marshes, concentrations of all the metals, except Cu. Zn, and Cd, exceeded 60% in the residual fraction as well. In the sediments from the Bay of Cádiz and Barbate River salt marshes, the main bioavailable metals were Mn and Cd; in those from the Odiel River salt marshes, the main bioavailable metals were Zn and Cd, respectively. The environmental risk was determined by employing the environmental risk factor (ERF), defined as ERF = (CSQV - Ci/CSQV), where Ci is the heavy metal concentration in the first four fractions and CSQV is concentration sediment quality value (the highest concentration with no associated biological effect). Our results showed that the sediments from the Cádiz Bay and Barbate River salt marshes do not constitute any environmental risk under the current natural conditions. In contrast, in the Odiel River salt marshes, Cu, Zn, and Pb yielded ERFs of less than zero at several sampling stations and, consequently, pose a potential threat for the organisms in the area. This is a consequence of the high levels of metals in the area derived from the mining activity (pyrite) and industrial activities and the association of these heavy metals with more labile fractions of the sediments.

Biological Availability↗

PubMed2004

The effects of decanted sediments on embryogenesis in oysters (Crassostrea gigas).

Sediments act as sinks for contaminants of natural and anthropogenic origin, constituting a risk to the living organisms. In this study, sediments were collected from three sites on the coast of southwest France. The objective of this research was to determine the effects of sediments on embryonic development of bivalves and to identify precisely when the contaminants affect the embryos and induce them to develop in an abnormal way. The toxicity of decanted sediments and overlying waters were assessed using the oyster embryo bioassay. The physical characteristics and contaminant levels in the sediments were measured, including polycyclic aromatic hydrocarbon (PAH) and metal concentrations. Despite contaminant concentrations for PAH and metals only exceeding the effects range-low levels, all decanted sediments tested induced deleterious effects on the embryonic development of oysters, while no significant abnormalities were observed for overlying waters. The study results suggest that abnormal larvae mainly are caused by direct contact with contaminated sediments.

Animals↗

PubMed2004

Modeling the fate of polychlorinated biphenyls in the inner Oslofjord, Norway.

A dynamic, segmented, multimedia fate and transport model has been developed, evaluated, and applied to gain insight regarding the behavior of seven polychlorinated biphenyl (PCB) congeners in the Inner Oslofjord (Norway). A comparison with a dated sediment core reveals that the model is not capable of reproducing some key features of the observed, historical, long-term trend in sediments, although better agreement is observed for six of seven PCB congeners over the last two decades. The model also underestimates the concentrations of PCBs in surface sediments in areas adjacent to the city of Oslo (Norway). In general, deviations between modeled and observed concentrations indicate that the historical emissions and discharges of PCBs are not sufficiently characterized and described. Net fluxes predicted by the model suggest that several congeners may have experienced a reversal of air-water and seawater-sediment exchange during the last decade or even earlier. The present study further suggests that the benefit of the proposed removal of the most contaminated sediments of the Inner Oslofjord needs to be assessed, with consideration of the relative contribution of current atmospheric inputs as well as the leaching of PCBs from less contaminated sediments.

Air↗