Identification of hot spots within harbour sediments through a new cumulative hazard index. Case study: Port of Bari,Italy

While numerous quality guidelines unquestionably drive the management of harbour sediments, port managers increasingly require easy-to-use tools supporting them in assessing the sediment quality. In this work, a new hazard index, named cumulative Normalized and Weighted Average Concentration (c_NWAC), is proposed, considering the concentrations of main hazardous, toxic and bio-accumulative sediment contaminants. This index is an upgraded version of the previously introduced NWAC index, which considered only the metal concentrations. The c_NWAC values range from 0 to 10 scores, and their visualization on a colour base code map leads to an easy identification of hotspots. The applicability of the new index was verified using a dataset derived from the analyses of 42 samples collected at different depths of the seabed of the Port of Bari (Italy). The concentrations of 58 parameters were considered, namely 11 metals and metalloids, 17 congeners of polychlorinated biphenyls (PCBs), 16 congeners of polycyclic aromatic hydrocarbons (PAHs), further 11 organic micropollutants, total organic carbon (TOC) and nutrients (N_tot, P_tot). For the study area, the obtained c_NWAC values resulted well correlated to the corresponding values of the commonly used mean Effects Range Median quotient (mERMq), and similar hazard categories were developed for the new index, even if the latter do not necessarily explain the real sediment toxicity, because they were derived from a different sediment dataset and different test species.Moreover, the hazard predictive ability of the new index was verified (with satisfactory results) by testing the considered samples by eco-toxicological assays, using three different biological species, and comparing the obtained results to the corresponding hazard categories developed for c_NWAC.     

Assessment of possible sediment toxicity of contaminated sediments in Port Jackson, Sydney, Australia

A considerable amount of chemical data is available for surficial sediments in Port Jackson. Some of the highest concentrations of heavy metals, organochlorines and polycyclic aromatic hydrocarbons of any capital port occur in sediments mantling shallow tributaries and embayments close to central Sydney. However, these data have limited ability to predict adverse effects on living resources and in the absence of toxicological data, sediment quality guidelines (SQG) have been used to assess the possible adverse biological effects of sedimentary contaminants in this estuary. Several SQGs are currently available for both fresh and marine environments, but the scheme used in the current study is based on empirical analysis of matching chemical and biological data compiled by the National Oceanographic and Atmospheric Administration (NOAA) in the U.S. The NOAA SQG can be used to assess individual chemicals, or to estimate the probability of acute sediment toxicity by calculating `mean quotients' for a large range of contaminants. Although many individual chemicals in sediment exceed SQG over extensive parts of Port Jackson, `mean quotient' results suggest that only a small proportion (1%) of the harbour may be highly toxic (74% probability of toxicity). However, sediment in a considerably larger proportion of the port (almost 25%) is estimated to have a 49% probability of being toxic using the `mean quotient' approach. These results are indicative at best and contemporaneous chemical/biological/ecotoxicological studies are needed to verify the applicability of SQG developed in the U.S. for use outside North America and site specific studies of this type are still required to determine the toxicity of sediments in Port Jackson.     

The influence of earthquakes on large lacustrine ecosystems, with particular emphasis on Lake Sevan, Armenia

This paper discusses the influence of earthquakes on large water ecosystems, with particular emphasis on Lake Sevan, Armenia. Earthquakes impact on large lacustrine ecosystems in seismically active areas in a number of ways, including chemistry and lake dynamics. Conclusions are drawn from a large database that includes biological, hydrological, geochemical and seismic information. Strong earthquakes change the water chemistry and pH of the lake and consequently the chemical and biological processes that take place in the lake bed sediments. Analysis of historical earthquakes shows their influence on the organic carbon in the sediments, the changes of the lake dynamics and variations in bacteria, phytoplankton and zooplankton at the base of the food chain.     

Bioavailability of Soil-Borne Chemicals: Abiotic Assessment Tools

The abiotic tools that are available, or under development, for evaluating the oral and dermal bioavailability of contaminants from soils are described in this article. These tools generally rely on one of two approaches: (1) characterizing the form of the contaminant and the chemical binding of the contaminant to the soil matrix, and (2) chemical extractions intended to evaluate the fraction of the chemical that would be liberated in biological fluids (gastrointestinal fluid or sweat). For the purpose of human health risk assessment, abiotic methods to estimate the bioavailability of inorganic contaminants in soil are considered generally to be “screening” level tools at this time. Development work for physiologically based extraction tests (PBETs) is ongoing for many inorganic contaminants, and these methods hold great promise for eventual use in making quantitative bioavailability adjustments in risk assessment. The availability of abiotic tools to evaluate the bioavailability of organic contaminants from soils lags behind that for metals, due to the difficulty in conducting in vivo bioavailability studies with organic compounds and their complex interactions with soil. However, considerable research is being conducted in this field, and new assessment tools are being validated for use in human health risk assessment.     

Invasion in tidal zones on complex coastlines: modelling larvae of the non‐native Manila clam,Ruditapes philippinarum,in the UK

Aim To evaluate whether natural larval transport and behaviour alone can explain the pattern of invasion and establishment of the non‐indigenous Manila clam, Ruditapes philippinarum ( Adams & Reeve, 1850 ), and its spread beyond the point of introduction in the UK. Location The study is focused on Poole Harbour, south England, the point of introduction of the Manila clam in the UK. Methods We use fine‐resolution hydrodynamic models coupled with a water salinity model and an individual behaviour model of Manila clam larvae. The model was informed by experimental studies on the vertical response of larvae to salinity and field studies of the species in its natural and new environments. Results Variations in the behavioural response of larvae to salinity in the model considerably affected the retention of clam larvae within the harbour. High levels of predicted larval retention occurred in two of five zones in the harbour when the salinity target was set at 17 practical salinity units. Persistently high densities of adult clams and recruits are accurately predicted in these regions. Main conclusions Even within a relatively small region such as Poole Harbour, there is both localized retention of larvae or ‘closed’ areas and areas that are considerably more ‘open’ and potentially connected. The behavioural response of larvae to salinity significantly affected the degree of retention and ‘openness’ of the harbour to this species. Although, through natural transport, larvae could theoretically reach the next available habitat within the duration of their pelagic stage our study indicates that areas of sufficiently reduced salinity may be necessary for sufficient retention, recruitment and establishment of new adult populations in estuaries. High resolution hydrodynamic models, coupled with larval behaviour, can accurately simulate and predict biological invasion along complex coastlines and contribute to risk assessment of the introduction of non‐indigenous species for aquaculture and spatial management of marine protection.     

Calculating Background Levels for Ecological Risk Parameters in Toxic Harbor Sediment

Establishing background levels for biological parameters is necessary in assessing the ecological risks from harbor sediment contaminated with toxic chemicals. For chemicals in sediment, the term contaminated is defined as having concentrations above background and significant human health or ecological risk levels. For biological parameters, a site could be considered contaminated if levels of the parameter are either more or less than the background level, depending on the specific parameter. Biological parameters can include tissue chemical concentrations in ecological receptors, bioassay responses, bioaccumulation levels, and benthic community metrics. Chemical parameters can include sediment concentrations of a variety of potentially toxic chemicals. Indirectly, contaminated harbor sediment can impact shellfish, fish, birds, and marine mammals, and human populations. This paper summarizes the methods used to define background levels for chemical and biological parameters from a survey of ecological risk investigations of marine harbor sediment at California Navy bases. Background levels for regional biological indices used to quantify ecological risks for benthic communities are also described. Generally, background stations are positioned in relatively clean areas exhibiting the same physical and general chemical characteristics as nearby areas with contaminated harbor sediment. The number of background stations and the number of sample replicates per background station depend on the statistical design of the sediment ecological risk investigation, developed through the data quality objective (DQO) process. Biological data from the background stations can be compared to data from a contaminated site by using minimum or maximum background levels or comparative statistics. In Navy ecological risk assessments (ERA's), calculated background levels and appropriate ecological risk screening criteria are used to identify sampling stations and sites with contaminated sediments.     

基于PSR模型的国家公园综合灾害风险评估指标体系构建

灾害会对社会-生态系统产生严重影响,造成重大的社会、经济、环境等方面的损失,科学地对灾害风险进行评估是进行防灾减灾的基础工作。自然保护地是区域灾害风险管理热点地区,在国家公园体制试点建设与自然保护地体系改革中,国家公园作为保护重要生态系统并保障全民公益性的重要的自然保护地类型之一,管理目标的多样性,决定了其具有多风险源-多受体的灾害风险特征,因此,进行全面有效的灾害风险评估是支持国家公园生态系统管理、游客管理、社区管理等具体管理目标的必要环节。在明确国家公园灾害风险的特征与内涵的基础上,以国际减灾署灾害风险定量评估框架为依据,细分灾害风险源和风险受体,然后针对国家公园不同类型的灾害风险受体,以灾害风险源的危险性与灾害风险受体的脆弱性(包含敏感性、暴露性和适应性)衡量灾害风险度,结合压力-状态-响应(Pressure-State-Response, PSR)模型,构建了适用于国家公园综合灾害风险管理的评估指标体系,旨在为国家公园的灾害风险管理提供理论基础和科学依据,服务于国家公园多元化管理目标。     

Analysis of biological features associated with meiotic recombination hot and cold spots in Saccharomyces cerevisiae

Meiotic recombination is not distributed uniformly throughout the genome. There are regions of high and low recombination rates called hot and cold spots, respectively. The recombination rate parallels the frequency of DNA double-strand breaks (DSBs) that initiate meiotic recombination. The aim is to identify biological features associated with DSB frequency. We constructed vectors representing various chromatin and sequence-based features for 1179 DSB hot spots and 1028 DSB cold spots. Using a feature selection approach, we have identified five features that distinguish hot from cold spots in Saccharomyces cerevisiae with high accuracy, namely the histone marks H3K4me3, H3K14ac, H3K36me3, and H3K79me3; and GC content. Previous studies have associated H3K4me3, H3K36me3, and GC content with areas of mitotic recombination. H3K14ac and H3K79me3 are novel predictions and thus represent good candidates for further experimental study. We also show nucleosome occupancy maps produced using next generation sequencing exhibit a bias at DSB hot spots and this bias is strong enough to obscure biologically relevant information. A computational approach using feature selection can productively be used to identify promising biological associations. H3K14ac and H3K79me3 are novel predictions of chromatin marks associated with meiotic DSBs. Next generation sequencing can exhibit a bias that is strong enough to lead to incorrect conclusions. Care must be taken when interpreting high throughput sequencing data where systematic biases have been documented.     

A review of assessment and remediation strategies for hat spot sediments

Sediments at the extreme end of the scale of contamination, designated as hot spot sediments, are considered. The characterization of such hot spots, and an approach for the quantitative assessments of the behaviour and fate of pollutants in such sediments are covered. Experiments with sediments containing extreme levels of heavy metals showed release rates of 56 mg m^–2 d^–1 of dissolved zinc and 0.004 mg m^–2 d^–1 of dissolved mercury. When these sediments were resuspended, the dissolved fluxes were increased by a factor of 2.2 and 128 for zinc and mercury, respectively. The biological implications of hot spot sediments are dealt with, since sediments are an important habitat for many organisms. Various alternatives for clean-up operations including dredging and capping are discussed.     

Metal concentrations in urban riparian sediments along an urbanization gradient

Urbanization impacts fluvial systems via a combination of changes in sediment chemistry and basin hydrology. While chemical changes in urban soils have been well characterized, similar surveys of riparian sediments in urbanized areas are rare. Metal concentrations were measured in sediments collected from riparian areas across the urbanization gradient in Baltimore, MD. Average metal concentrations are similar to those observed in other regional studies. Two important spatial patterns are evident in the data. First, calcium concentrations double across the urbanization gradient, regardless of changes in underlying geochemistry at the boundary between the Eastern US Piedmont and Coastal Plain physiographic provinces. Alkali-earth metal ratios indicate that the additional Ca is very pure and possibly arises from cement common to urban systems. Second, hot spots of trace metals typically associated with urban systems (e.g., Cu, Zn, and Pb) occur in areas that have been artificially filled to create additional real estate in high land value areas. Together, these data indicate that riparian sediments exhibit unexpected patterns of metal contamination. If these sediments are remobilized, during events such as droughts or floods, this contamination may perpetuate legacy impacts to ecosystem health from a history of fluvial contamination.     

An assessment of the potential impact of dredging activity on the Tamar Estuary over the last century: Bathymetric and hydrodynamic changes

The Tamar Estuary, S.W. England, is a commercial and military port and the site of a major naval dockyard. Parts of the estuary require regular maintenance dredging and some capital dredging has been undertaken. The estuary is also assigned Special Area of Conservation (SAC) status under the European Habitats Directive and is an important site for migrating wildfowl and wading birds. As part of an assessment undertaken for a consortium of the port operators and regulatory authorities, we have analysed the ecological, physical, chemical and socio-economic impacts of dredging on the Tamar Estuary ecosystem. This paper focuses on the physical changes through the analysis of historical survey data and the use of hydrodynamic modelling. The objective was to evaluate whether dredging has influenced the estuary morphology or hydrodynamic regime and thus impacted on the ecological habitat. Bathymetric survey data collected between 1895 and 1968 were compared with multi-beam echo sounder data obtained in 2001. The paper survey records were digitised, geo-referenced and adjusted to the modern datum and units. The accuracy and limitations of this approach are discussed. Both sets of data were contoured and analysed using a GIS package. Comparisons between 1895 and 2001 hydraulics were made using a 1-D hydrodynamic and sediment transport model set up for the bathymetry at those times but ‘driven’ using a single, common, year-long data set for tides and river flows. The results suggest that although the deep channel in the region that is mainly south of the Tamar road bridge, is on average 0.5 m deeper in 2001 than it was in 1895, this has had a negligible effect on the area of intertidal mud and, thus, on habitat available for wading birds, and minimal impact on the large-scale hydrodynamics of the estuary.     

Contamination of a dredged material disposal site La Rochelle Bay,France .The use of the acetylcholinesterase activity of Mytilus edulis L. as a biomarker of pesticides: the need for a critical approach

A single aspect of the toxic impact of a dredged material disposal site located near a mussel-farming zone was followed for eight months. Acetylcholinesterase activity (AChE) of Mytilus edulis was investigated as a biomarker for possible contamination by neurotoxic compounds (carbamates and/or organophosphorous pesticides). Our observations showed that the enzymatic activities (including AChE) of these harbour mussels were decreased in sites directly and indirectly influenced (according to hydrodynamic conditions) by the dumping of dredged sediments, suggesting possible contamination by pesticides. The strong correlations observed between AChE activity and growth parameters (length and weight) seems to show, however, that the enzyme activity is also indirectly controlled through growth restriction, which may imply limitation of the development of the nervous system in juveniles. The concentration of total proteins, as well as the spawning process also seem to disturb the assessment of AChE activity. These field observations clearly indicate that the use of this enzyme activity as a biomarker should proceed with caution. For example, the seasonal variability of such activity should be taken into account in a biomonitoring programme.     

Detection of genotoxins in the marine environment: adoption and evaluation of an integrated approach using the embryo-larval stages of the marine mussel, Mytilus edulis

In genetic ecotoxicology or eco-genotoxicology, there is lack of well-validated systems which could demonstrate the utility of multiple endpoints in environmental quality assessment. For an evaluation of genotoxic potential of heterogeneous marine sediment samples collected from a small fishing harbour in the UK, an in vivo test system using embryo-larval stages of the common mussel, Mytilus edulis was validated against direct and indirect acting reference mutagens. The system appeared to be sensitive and reproducible for cytogenetic endpoints analysed (sister chromatid exchanges (SCEs) and chromosomal aberrations (CAbs)). Following validation and chemical characterisation of the environmental samples, multiple endpoints were measured. Determination of the maximum tolerated dose (MTD) was carried out as a measure to determine cytotoxic effects as a confounding factor for genotoxicity, based on developmental and cytotoxic (in terms of proliferative rate index or PRI) effects. Evaluation of the genotoxic potential of the samples gave a positive response for all the endpoints tested, linking different levels of biological organisation (i.e., chromosomal, cellular and organismal) for the observed effects. The study also emphasises the need for the assessment of the short and long-term impacts of dredge disposal on marine biota by including laboratory-based bioassays and incorporating an integrated approach which could yield as much useful information as possible in overall hazard and risk assessment for aquatic genotoxicity.     

Field Characterization of Potential Reference Sediments in the Gulf of Mexico: Chemical and Biological Quality

Baseline information on the chemical and biological quality of sediments is provided for six coastal locations in the northern Gulf of Mexico, which were considered possible candidates for regional reference areas. Chemical quality, toxicity and benthic community composition were determined for sediments collected three times from each of 12 sites during an approximate one-year period. Potential contaminants in the usually sand-dominated sediments exceeded individual threshold effects level guidelines proposed for Florida coastal areas in approximately 31% of the samples collected from 8 of 12 sites. No probable effects level guidelines were exceeded. Acute toxicity occurred in 16% or less of the sediment samples and no significant chronic toxicity was observed to the infaunal amphipod, Leptocheirus plumulosus. Approximately, 11% and 17% of the sediments were classified as poor or marginal, based on low benthic taxa abundance and diversity index values, respectively. Sediment quality at many sites was less degraded than that for nearby coastal areas receiving point and non-point source contaminants, which suggests their suitability to serve as reference sediments although further confirmation is recommended. In a broader context, the results of this survey reflect the complexity in field verification of reference conditions for near-coastal sediments. This is attributable largely to the natural variability in their physical, biological, and chemical characteristics and to the lack of biocriteria for benthic macro and meiofauna.     

Harbour and coastal sediment chemistry and toxicity: a preliminary assessment of dredging activities

In a project to assess the environmental impact of dumping contaminated harbour material in a coastal marine area of the Northern Tyrrhenian Sea, sediments from different sites (harbour, dumping and uncontaminated sites) were sampled in December 1993 and February 1994. In order to evaluate sediment quality, concentrations of heavy metals (Cd, Pb, Cr and Hg) and polycyclic aromatic hydrocarbons (PAHs) were determinated and toxicity tests were carried out using the sea urchin Paracentrotus lividus. Interstitial water and the sea water overlying sediments (bedded phase and suspended phase) were tested for their effects on fertilization and embryogenesis. Sediment texture was also considered. Metal concentrations, particularly cadmium content, and PAH total concentrations, in harbour sediments were generally higher than in offshore samples. No significant reductions in fertilization were observed. However, effects on the embryonic development were evident and interstitial water toxicity was shown to be greater than either bedded or suspended exposures.     

Efficient localization of hot spots in proteins using a novel S-transform based filtering approach

Protein-protein interactions govern almost all biological processes and the underlying functions of proteins. The interaction sites of protein depend on the 3D structure which in turn depends on the amino acid sequence. Hence, prediction of protein function from its primary sequence is an important and challenging task in bioinformatics. Identification of the amino acids (hot spots) that leads to the characteristic frequency signifying a particular biological function is really a tedious job in proteomic signal processing. In this paper, we have proposed a new promising technique for identification of hot spots in proteins using an efficient time-frequency filtering approach known as the S-transform filtering. The S-transform is a powerful linear time-frequency representation and is especially useful for the filtering in the time-frequency domain. The potential of the new technique is analyzed in identifying hot spots in proteins and the result obtained is compared with the existing methods. The results demonstrate that the proposed method is superior to its counterparts and is consistent with results based on biological methods for identification of the hot spots. The proposed method also reveals some new hot spots which need further investigation and validation by the biological community.     

Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state

Characterization of binding hot spots of protein interfaces is a fundamental study in molecular biology. Many computational methods have been proposed to identify binding hot spots. However, there are few studies to assess the biological significance of binding hot spots. We introduce the notion of biological significance of a contact residue for capturing the probability of the residue occurring in or contributing to protein binding interfaces. We take a statistical Z-score approach to the assessment of the biological significance. The method has three main steps. First, the potential score of a residue is defined by using a knowledge-based potential function with relative accessible surface area calculations. A null distribution of this potential score is then generated from artifact crystal packing contacts. Finally, the Z-score significance of a contact residue with a specific potential score is determined according to this null distribution. We hypothesize that residues at binding hot spots have big absolute values of Z-score as they contribute greatly to binding free energy. Thus, we propose to use Z-score to predict whether a contact residue is a hot spot residue. Comparison with previously reported methods on two benchmark datasets shows that this Z-score method is mostly superior to earlier methods. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.     

Protected and threatened components of fish biodiversity in the Mediterranean sea

The Mediterranean Sea (0.82% of the global oceanic surface) holds 4%-18% of all known marine species (~17,000), with a high proportion of endemism [1, 2]. This exceptional biodiversity is under severe threats [1] but benefits from a system of 100 marine protected areas (MPAs). Surprisingly, the spatial congruence of fish biodiversity hot spots with this MPA system and the areas of high fishing pressure has not been assessed. Moreover, evolutionary and functional breadth of species assemblages [3] has been largely overlooked in marine systems. Here we adopted a multifaceted approach to biodiversity by considering the species richness of total, endemic, and threatened coastal fish assemblages as well as their functional and phylogenetic diversity. We show that these fish biodiversity components are spatially mismatched. The MPA system covers a small surface of the Mediterranean (0.4%) and is spatially congruent with the hot spots of all taxonomic components of fish diversity. However, it misses hot spots of functional and phylogenetic diversity. In addition, hot spots of endemic species richness and phylogenetic diversity are spatially congruent with hot spots of fishery impact. Our results highlight that future conservation strategies and assessment efficiency of current reserve systems will need to be revisited after deconstructing the different components of biodiversity.     

Bioassay responses to sediment elutriates and multivariate data analysis for hazard assessment of sediment-bound chemicals

A sediment study, involving both chemical and biological analyses, was carried out in the Hamburg harbour area. A total of 71 stations were sampled during 1988 and the sediments extracted using a 1:4 sediment:water ratio either with or without an addition of a water-soluble detergent to solubilize organic compounds. The resulting extracts were applied in algal and bacterial assays to measure toxicity. A principal components analysis showed that no single bioassay explained all the variation in toxicity among the locations studied. Hierarchical cluster analysis was used to rank sediments into four groups based on their toxicity. The relationship of toxic responses to the chemistry of the sediments was determined using varimax factor analysis. One factor was loaded with algal responses and mercury contents of sediments, another with bacterial responses and Lindane contents of sediments.