Prokaryotic diversity,composition structure,and phylogenetic analysis of microbial communities in leachate sediment ecosystems

In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.     

Improving the Electrokinetic Remediation of Nickel-, Cadmium-, and Lead-contaminated Sediment

In this work, the simultaneous application of bipolar electrodes and a longer cathodic compartment length without agents addition was used as an enhanced electrokinetic treatment of Ni-, Cd-, and Pb-contaminated sediment. Conventional and enhanced treatments were investigated and their efficacy assessed by comparing the residual metals content in the sediment with values given by Dutch standards. After conventional treatment removals of 20%, 19%, and 31% for Ni, Cd, and Pb were achieved, whereas the enhanced treatment achieved removal efficacies of 36% for Ni, 42% for Cd, and 43% for Pb. Results indicate that the simultaneous application of the techniques mentioned is effective for removing Ni and Pb whereas Cd was not removed to the desired level. Here we show that the addition of chemicals is not necessary to increase the efficacies of electrokinetic sediment treatments, so the simultaneous application of the techniques mentioned can be described as environmentally friendly.     

A comparison of methods of determining organic carbon in marine sediments,with suggestions for a standard method

The yield of organic C or total organic matter from a standard carbonate-free marine sediment containing 23.04% N-acetyl glucosamine (10% organic C) was determined using 1) a CHN analyzer on untreated sediment, 2) CHN analysis of acidified and filtered sediment, 3) CHN analysis of acidified centrifuged sediment, 4) wet oxidation by the Walkley and Black method, and 5) loss on ignition at 475–500°C. 100% of the organic C added was recovered by CHN analysis of untreated sediment, but after treatment with acid (necessary to remove carbonates from most sediments) only 0.19% and 1.32% of the C added could be recovered. Wet oxidation yielded only 76.6% organic C. Loss on weight after combustion in a muffle furnace yielded 100% of the total organic matter. It is very difficult to avoid carbonate interference if simple techniques of analysis are used. For most work by marine ecologists organic carbon and nitrogen may be measured by a combination of CHN analysis and loss of weight on ignition of sediments freed of organic matter by precombustion below 500°C.     

Quantifying Burial,the Transport of Matter from the Lake Biosphere to the Geosphere

Burial is one of the most fundamental processes in contexts of massbalance calculations for substances (such as nutrients, organics, metals and radionuclides) in lakes. Substances can leave a lake by two processes, outflow, i.e., the transport to a downstream system, and burial, i.e., the transport by sedimentation from the lake biosphere to the geosphere. This work gives for the first time, to there best of the author's knowledge, a review on the factors and processes regulating burial and presents a general model for burial. This approach accounts for bottom dynamic conditions (i.e., where areas of fine sediment erosion, transport and accumulation prevail), sedimentation, bioturbation, mineralisation, and the depth and age of the bioactive sediment layer. This approach has been critically tested with very good results for radiocesium, radiostrontium, many metals, calcium from liming and phosphorus, but it has not been presented before in a comprehensive way. This model for burial is meant to be used in massbalance models based on ordinary differential equations (i.e., box models) in contexts where burial is not a target y‐variable but a necessary model variable (an x‐variable). This means that there are also specific demands on this approach, e.g., it must be based on readily accessible driving variables so that it is not too difficult to use the model in practice within the context of an overall lake model. The factors influencing burial, e.g., the deposition of materials and the depth of the bioactive sediment layer, are also needed in calculations of sediment concentrations and to determine amounts of substances or pollutants in sediments. To carry out such calculations, one also needs information on sediment bulk density, water content and organic content. This paper also presents new empirical models for such calculations to be used in the new model for burial.     

Versatile habitat conditioning by damselfish cultivating turf algae on giant clams

In this paper, a monitoring and modelling concept for ecological optimized harbour dredging and fine sediment disposal in large rivers is presented. According to the concept, first a preliminary assessment should be performed previous to the dredging and dumping procedure to derive knowledge about the current status in hydrodynamics, morphology and instream habitat quality. During the performance of the maintenance work, a high-resolution monitoring program has to be organized to measure flow velocities, the suspended sediment concentrations and the extent of the occurring plume. These data can then be compared with natural suspended sediment conditions and serve as input data for numerical sediment transport modelling. Furthermore, bathymetric surveys and biotic sampling enable the detection of possible effects of dredging and disposal in the post-dumping stage. Based on sediment transport modelling approaches, short- to mid-term developments of the sediment plume can be predicted with an additional and final habitat evaluation at the end of the project. This concept was applied and optimized during the maintenance work at the case study winter harbour Linz at the Danube River. The findings of the presented study highlight the necessity of integrated monitoring and modelling approaches for harbour dredging especially in large river systems.     

Tidal flows and sediment budgets for a salt-marsh system,Essex, England

Studies of tidal flows in salt-marsh creeks in Essex, England, show large variations in water velocity during different tidal cycles, particularly between tides below, at, and above marsh level. Water level, velocity and suspended sediment concentration have been monitored at 5-min intervals during 700 tidal cycles during the year March 1982–March 1983, and the data are being used to calculate sediment budgets for the creek system studied. Completed analyses for two of the tidal cycles show a large positive sediment flux. Because of the importance of velocity in controlling total discharge through a creek cross-section, and hence its effect on total sediment movement, we cannot extrapolate from these two below-marsh tides to any general conclusions about marsh erosion or accretion. We use these preliminary data both to demonstrate our methods and to indicate some of the complexities involved in the analysis.Acknowledgements: This work has been supported by the Natural Environment Research Council. We thank the Philip Lake Fund for financial assistance and the Department of Geography, Cambridge University, for much material support. Mr D. J. Fisher kindly gave access to his land, and Mr W. Bailey helped us greatly. We also thank Mr A. St Joseph for his help, Mr M. Diver for practical support, and Dr J. S. Pethick for discussion.     

Characterization of Depth-Related Microbial Community Activities in Freshwater Sediment by Combined Method

Currently there are very few researches on studying the vertical changes of metabolic and thermodynamic properties of microbial communities in freshwater lake sediment. In this work, a multi-channel microcalorimetric system was applied to investigate both the metabolism and thermodynamic properties of 0–35 cm sediment cores from Lake Honghu (Jingzhou, Hubei Province, China). It is suggested that the catastrophic flood in 1998 had changed the structure of the 20–25 cm sediment layer. In this layer, both the physicochemical properties of sediment and the thermodynamic activities of microorganisms exhibit distinct differences from other layers. It displays the highest TOC, TN and C/N values. The power-time curves of microcalorimetric measurement on the sediment samples were plotted to illustrate their microbial activities. The 20–25 cm sediment layer showed the lowest microbial activities with a maximum heat flow rate of 56.97 μW, a growth rate constant of 0.06 h ^?1 and the time to reach the peak was 98 h. A positive correlation (r= 0.972, P< 0.001) was found between the cell specific metabolic enthalpy change rate (ΔH₀ ) and the TOC of the sediment samples. ΔH₀ could indicate the utilization efficiency of carbon source which is not affected by the biomass but relies on the intrinsic properties of sediment. Our work shows that the higher the TOC in sediment; the lower the efficiency in assimilating carbon into biomass by the microbes.     

Increase in Alphaproteobacteria in association with a polychaete,Capitella sp. I,in the organically enriched sediment

We conducted bioremediation experiments on the organically enriched sediment on the sea floor just below a fish farm, introducing artificially mass-cultured colonies of deposit-feeding polychaete, Capitella sp. I. To clarify the association between the Capitella and bacteria on the efficient decomposition of the organic matter in the sediment in the experiments, we tried to identify the bacteria that increased in the microbial community in the sediment with dense patches of the Capitella. The relationship between TOC and quinone content of the sediment as an indicator of the bacterial abundance was not clear, while a significant positive correlation was found between Capitella biomass and quinone content of the sediment. In particular, ubiquinone-10, which is present in members of the class Alphaproteobacteria, increased in the sediment with dense patches of the Capitella. We performed denaturing gradient gel electrophoresis (DGGE) analyses to identify the alphaproteobacterial species in the sediment with dense patches of the worm, using two DGGE fragments obtained from the sediment samples and one fragment from the worm body. The sequences of these DGGE fragments were closely related to the specific members of the Roseobacter clade. In the associated system with the Capitella and the bacteria in the organically enriched sediment, the decomposition of the organic matter may proceed rapidly. It is very likely that the Capitella works as a promoter of bacteria in the organically enriched sediment, and feeds the increased bacteria as one of the main foods, while the bacteria decompose the organic matter in the sediment with the assistance of the Capitella.     

Further experimental investigations on the formation of plant compression fossils

Experimental work has been conducted on the formation of plant compression fossils using a simple compression apparatus in which actual plant material was compressed in wet sediment. Pressure was applied through a single perforated piston which only allowed the passage of water upwards out of the compacting sediment. Several lines of investigation were followed to establish the principal factors that dictate the form of a plant compression fossil. It is demonstrated that these include the grain size and the compressibility of the sediment, the degree of sediment fill of hollow structures within the plant organ prior to the compression, and finally the rigidity or degree of decay of the plant tissues before the deformation. The results of this work indicate that the horizontal dimensions of the plant organ change during compression. This is directly related to the compressibility of the sediment the plant was buried in; stems buried in clay matrices increased in horizontal dimensions, whereas stems buried in sand matrices underwent reductions in horizontal dimensions. This is associated with the difference in the response of these sediments to the hydrostatic stress that exists within the system during the initial stages of compaction. The results of this experimental study are used to interpret the structure and form of some plant compression fossils.     

Sediment Transport Modeling: Calibration,Verification, and Evaluation

Numerical modeling of sediment transport in fluvial and estuarine systems can be a reliable way of predicting sediment mobility. If approached naïvely, however, such modeling can produce results that do not have sufficient accuracy or reliability to be useful in decision making or design regarding a range of remediation or stabilization alternatives. It is important to recognize the numerical modeling process as merely one step toward a more complete and balanced understanding of the fluvial or estuarine system in question. Other steps include qualitative and quantitative geomorphic and engineering analyses used to evaluate the accuracy and reliability of numerical modeling as part of a three-level approach to analyze sediment mobility and overall channel behavior and trends. It must first be recognized that attempting to quantitatively analyze sediment mobility involves developing and applying simplified mathematical algorithms to the complexities of continually varying hydrodynamic and sediment transport processes through natural or modified bodies of water. Accuracy in sediment modeling can only be assessed by comparing measured data to model results with accuracy being defined as the model results matching the data within some acceptable band of uncertainty. Reliability of a sediment model is the concept of dependability in reproducing the processes one is attempting to model and implies that a model includes appropriate mathematical expressions that cover the pertinent physical processes of hydrodynamics and sediment mobility. The concept of reasonableness in sediment modeling is the evaluation of results, when compared with other independent analyses in the application of the three-level process, provide an acceptable level of consistency and consensus of conclusions. The importance of modeling software selection, data quality, model calibration, verification, validation, and reasonableness of results are discussed along with two case studies.     

Effects of Native Plant Species,Mycorrhizal Inoculum,and Mulch on Restoration of Reservoir Sediment Following Dam Removal,Elwha River,Olympic Peninsula,Washington

As dams across the country continue to age, successful restoration of dewatered reservoirs remains a critical factor in decisions regarding dam removal. Freshly exposed reservoir sediment may not support rapid reestablishment of native plant species due to poor fertility or absence of arbuscular mycorrhizal fungi propagules. This field study evaluated treatment effects involving combinations of native plants, mycorrhizal inoculum, and mulch on restoration of dewatered reservoir sediment over 20 months. Most plants, even those uninoculated, became mycorrhizal. In all treatments, sediment pH decreased, as did nitrogen and organic matter, compared to original reservoir sediment, while aggregate stability doubled from original anaerobic sediment. Revegetated plots with mulch had significantly greater vegetation cover and more native volunteer species compared to plots without mulch. The planted mulch treatment also decreased plot runoff tenfold, reducing erosion to the same degree. Indicators suggest that the primary benefit of mulch resulted in increased moisture retention making the planted mulch treatment most successful for restoration of reservoir sediment due to extensive native plant growth, improved soil characteristics, and reduced runoff and erosion compared to nonmulched plots. While results from this plot‐scale study suggest commercial mycorrhizal inoculum is unnecessary since natural inoculum sources sufficiently colonized plants, reservoir‐scale restoration may require creation of additional source areas to encourage rapid reestablishment of native plants and mycorrhizal fungi.     

Cyst formation,sedimentation, and preservation: Factors affecting dinoflagellate assemblages in recent sediments from trondheimsfjord,Norway

Plankton records and 25 samples of Recent sediment from Trondheimsfjord and the adjoining shelf were studied to investigate production, sedimentation, and preservation of cysts, as factors which influence the eventual composition of dinoflagellate cyst assembleges. All sediment samples were examined for dinoflagellate cysts using routine semiquantitative palynological procedures. In addition, fjord sediments were subjected to a limited sediment analysis, and, for three samples, results from preparations both with and without acid treatments were compared. For the first time, cyst assembleges from Recent sediments were directly compared with extensive plankton records from overlying waters. Results indicate that approximately 20% of the 55 locally recorded dinoflagellate species contribute cysts to bottom sediments. Once formed, cysts behave as fine silt particles in the sedimentary regime, increasing in abundance as the percentage abundance of finer sediment increases, usually with increased water depth. Cyst-forming species are almost entirely restricted to a few genera, particularly Gonyaulax and Peridinium, within the order Peridiniales. For some groups, reasonably good correspondence was found between percentage abundances of dinoflagellates in plankton and their cysts in sediment, though plankton records covering at least five years were required to establish this. Gonyaulax grindleyi Reinecke (Von Stosch 1969) appeared to be consistently overrepresented by cysts in sediment relative to available plankton evidence; possible explanations are suggested. At least 30% of the cyst species present, including most Peridinium species, were eliminated, or rendered unreliable for semiquantitative palynology, by application of routine palynological preparation treatments. Such cysts may provide useful, non-quantitative, palynological information from Recent and possibly Quaternary sediments, but their persistence would seem unlikely. Thus, factors of preservation probably further restrict the dinoflagellate fossil record. Cyst assemblages from Trondheimsfjord are comparable with those previously recorded from the northeastern coast of U.S.A., and from Scotland and northeastern England. Fjord assemblages are dominated by small, simple, spinose cysts which would be regarded as acritarchs if culture experiments had not proved that they are dinoflagellate cysts. Much potential biogeographic and palaeoenvironmental information was included within the less abundant species.Attention is drawn to the role which future culture experiments may be expected to play in helping to resolve taxonomic difficulties currently affecting dinoflagellate studies. Palynological significance of results from the present study is discussed especially with reference to recent work by Von Stosch which strongly suggests that cysts may be hypnozygotes formed routinely in sexual cycles of dinoflagellates.     

Sediment resuspension and transport patterns on a fringing reef flat,Molokai, Hawaii

Corals are known to flourish in various turbid environments around the world. The quantitative distinction between clear and turbid water in coral habitats is not well defined nor are the amount of sediment in suspension and rates of sedimentation used to evaluate the condition of reef environments well established. This study of sediment resuspension, transport, and resulting deposition on a fringing reef flat off Molokai, Hawaii, uses a year of time-series data from a small, instrumented tripod. It shows the importance of trade winds and ocean wave heights in controlling the movement of sediment. Sediment is typically resuspended daily and the dominant controls on the magnitude of events (10–25 mg/l) are the trade-wind-generated waves and currents and tidal elevation on the reef flat. The net flux of sediment on this reef is primarily along the reef flat in the direction of the prevailing trade winds (to the west), with a secondary direction of slightly offshore, towards a zone of low coral abundance.These results have application to reef studies and reef management in other areas in several ways. First, the observed resuspension and turbidity results from fine-grained terrigenous sediment that appears to be trapped and recycled on the reef flat. Thus corals are subjected to light attenuation by the same particles repeatedly, however small the amount. Secondly, the measurements show high temporal variability (from daily to seasonal scales) of sediment resuspension, indicating that single measurements are inadequate to accurately describe conditions on a reef flat.Communicated by: P.K. Swart     

Characterization and Mapping of Contaminated Sediments,Windermere Arm,Hamilton Harbour,Ontario, Canada

Windermere Arm is a 50-ha narrow channel located in the south-eastern portion of Hamilton Harbour, which is designated by the International Joint Commission (IJC) as one of the primary Areas of Concern in the Canadian waters of the Great Lakes. Sediments within the Arm have historically been contaminated with metals, PAHs, and to a lesser extent, PCBs. Sedimentological, geotechnical and geochemical investigations have been undertaken to determine the degree and the spatial extent of contamination. The thickness of contaminated sediment and their degree of contamination vary widely within the study site. Information on the thickness of contamination obtained from logging and chemical analysis of sediment cores agrees in general with the results of in situ penetrometer testing. Concentrations of Zn and Pb in some sub-samples are above the Severe Effect Level (SEL) for benthos set by the Ontario sediment quality guidelines. On average, surficial sediments tend to have lower metal concentrations than deeper sediments, probably due to the reduction of industrial point discharges. Apart from the two main boat slips, concentrations of PAHs are relatively low and in agreement with previously reported values. In contrast, new results yield higher values of PCB concentrations than previously reported, and 21 sub-samples of surficial sediment analyzed yielded values greater than 1 μg/g. Results suggest that the majority of recent PCB loadings are entering the study site from nearshore industrial spills or dumping, despite the detection of trace amounts of PCBs in a nearby creek. Pronounced sediment disturbance noted in several cores suggests that more contaminated historical sediments are at risk of being disturbed and re-exposed to the water column.     

Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA Genes

Bacterial communities associated with seagrass bed sediments are not well studied. The work presented here investigated several factors and their impact on bacterial community diversity, including the presence or absence of vegetation, depth into sediment, and season. Double-gradient denaturing gradient gel electrophoresis (DG-DGGE) was used to generate banding patterns from the amplification products of 16S rRNA genes in 1-cm sediment depth fractions. Bioinformatics software and other statistical analyses were used to generate similarity scores between sections. Jackknife analyses of these similarity coefficients were used to group banding patterns by depth into sediment, presence or absence of vegetation, and by season. The effects of season and vegetation were strong and consistent, leading to correct grouping of banding patterns. The effects of depth were not consistent enough to correctly group banding patterns using this technique. While it is not argued that bacterial communities in sediment are not influenced by depth in sediment, this study suggests that the differences are too fine and inconsistent to be resolved using 1-cm depth fractions and DG-DGGE. The effects of vegetation and season on bacterial communities in sediment were more consistent than the effects of depth in sediment, suggesting they exert stronger controls on microbial community structure.     

Imaging Oxygen Distribution in Marine Sediments. The Importance of Bioturbation and Sediment Heterogeneity

The influence of sediment oxygen heterogeneity, due to bioturbation, on diffusive oxygen flux was investigated. Laboratory experiments were carried out with 3 macrobenthic species presenting different bioturbation behaviour patterns: the polychaetes Nereis diversicolor and Nereis virens, both constructing ventilated galleries in the sediment column, and the gastropod Cyclope neritea, a burrowing species which does not build any structure. Oxygen two-dimensional distribution in sediments was quantified by means of the optical planar optode technique. Diffusive oxygen fluxes (mean and integrated) and a variability index were calculated on the captured oxygen images. All species increased sediment oxygen heterogeneity compared to the controls without animals. This was particularly noticeable with the polychaetes because of the construction of more or less complex burrows. Integrated diffusive oxygen flux increased with oxygen heterogeneity due to the production of interface available for solute exchanges between overlying water and sediments. This work shows that sediment heterogeneity is an important feature of the control of oxygen exchanges at the sediment-water interface.     

全氟辛酸在沉积物-水界面污染及吸附迁移行为研究进展

全氟辛酸(PFOA)是一种重要的全氟化表面活性剂,具有环境持久性、高毒性和生物累积性等特征,成为当前备受关注的新污染物。沉积物是PFOA的重要环境储蓄库,被污染后的沉积物可作为长期污染源造成上覆地表水及周边地下水污染。本文结合近年来国内外研究,对地表水和沉积物中PFOA的来源、污染现状和界面吸附迁移行为进行了综述。结果表明: 地表水体和沉积物中PFOA最主要的污染来源为工业废水排放。全球范围地表水体和沉积物中PFOA污染水平普遍为ng·g^-1和ng·L^-1数量级,且国内部分地区污染形势更为严峻。沉积物组分、水化学条件、有机质及表面活性剂等因素均影响沉积物中PFOA的吸附行为,但目前在吸附主控机制方面仍然存在争议。沉积物中PFOA迁移行为的研究正处于起步阶段,相关报导还较为缺乏,对于迁移机理的认识还很不足,今后需在该方面加大研究力度。     

Recent Increases in Sediment and Nutrient Accumulation in Bear Lake, Utah/Idaho, USA

This study examines historical changes in sediment and nutrient accumulation rates in Bear Lake along the northeastern Utah/Idaho border, USA. Two sediment cores were dated by measuring excess ²¹⁰Pb activities and applying the constant rate of supply (CRS) dating model. Historical rates of bulk sediment accumulation were calculated based on the ages within the sediment cores. Bulk sediment accumulation rates increased throughout the last 100 years. According to the CRS model, bulk sediment accumulation rates were <25mgcm^?2year^?1 prior to 1935. Between 1935 and 1980, bulk sediment accumulation rates increased to approximately 40mgcm^?2year^?1. This increase in sediment accumulation probably resulted from the re-connection of Bear River to Bear Lake. Bulk sediment accumulation rates accelerated again after 1980. Accumulation rates of total phosphorus (TP), total nitrogen (TN), total inorganic carbon (TIC), and total organic carbon (TOC) were calculated by multiplying bulk sediment accumulation rates times the concentrations of these nutrients in the sediment. Accumulation rates of TP, TN, TIC, and TOC increased as a consequence of increased bulk sediment accumulation rates after the re-connection of Bear River with Bear Lake.     

The impact of the sand prawn Callianassa kraussi Stebbing on sediment turnover and on bacteria,meiofauna, and benthic microflora

Field cages were used to manipulate the density of the thalassinidean Callianassa kraussi Stebbing to test its effects on the turnover of sediment and on the abundance of benthic microflora, bacteria, and meiofauna. By introducing layers of stained sediment into the cages the rate of bioturbation could be quantified, and over a month averaged 59% turnover down to a depth of 30 cm (equivalent to a deposit of 12.14 kg · m ⁻² · day⁻¹ on the surface). Virtually no bioturbation occurred in cages lacking Callianassa, even although all other infaunal species had been left undisturbed in the cages. Benthic microalgae accumulated on the surface in the absence of Callianassa, but were relatively more abundant at depths of 15 to 25 cm in their presence. Even at this depth they were fully viable, presumably because the turnover of sediment brought them to the surface often enough to maintain them. Bacterial numbers increased between 30 and 100% in the presence of Callianassa, and were concentrated around the linings of their burrows. Meiofaunal numbers declined in proportion to the density of Callianassa, although the reason for this decline is unknown. Taken in conjunction with published work on the detrimental effects Callianassa spp. have on corals, suspension-feeders and seagrasses, these results emphasize the powerful rôle Callianassa plays in structuring the communities of soft sediments.