Genome resources have advantages for understanding diverse areas such as biological patterns and functioning of organisms. Omics platforms are useful approaches for the study of organs and organisms. These approaches can be powerful screening tools for whole genome, proteome, and metabolome profiling, and can be used to understand molecular changes in response to internal and external stimuli. This methodology has been applied successfully in freshwater model fish such as the zebrafish Danio rerio and the Japanese medaka Oryzias latipes in research areas such as basic physiology, developmental biology, genetics, and environmental biology. However, information is still scarce about model fish that inhabit brackish water or seawater. To develop the self-fertilizing killifish Kryptolebias marmoratus as a potential model species with unique characteristics and research merits, we obtained genomic information about K. marmoratus. We address ways to use these data for genome-based molecular mechanistic studies. We review the current state of genome information on K. marmoratus to initiate omics approaches. We evaluate the potential applications of integrated omics platforms for future studies in environmental science, developmental biology, and biomedical research. We conclude that information about the K. marmoratus genome will provide a better understanding of the molecular functions of genes, proteins, and metabolites that are involved in the biological functions of this species. Omics platforms, particularly combined technologies that make effective use of bioinformatics, will provide powerful tools for hypothesis-driven investigations and discovery-driven discussions on diverse aspects of this species and on fish and vertebrates in general.

To examine the influence of habitat alteration by tideflat reclamation on the physiological ecology of Ruditapes philippinarum, seasonal variations in its condition, gross biochemical composition, and reproductive cycle were compared for a yearly cycle between a reclaimed flat (Gomsohang, GS) and a natural flat (Hajun, HJ) in Gomso Bay, Korea. Concentrations of chlorophyll a and seston (as well as its energy value as food available to the clam) were consistently higher at HJ than at GS. Condition, dry tissue weight, and energy reserves (proteins and carbohydrates) of the clams were much higher at HJ than at GS during spring–summer, when fast growth and gametogenic development occur. Furthermore, their spring gametogenic development and spawning were advanced at HJ compared with GS. Our results suggest that the Manila clam encounters nutritionally stressful environmental conditions in altered habitats after tideflat reclamation that lead to lowered nutrient accumulation and a changing reproductive cycle.

Since the 1970s, the catch of Tairagi and Agemaki shellfish that inhabit the shallow sediments of the Ariake Sea of Japan has fallen dramatically. This is partly accounted for by the Isahaya land reclamation dike project and by the increasingly frequent local red tides. A recent survey of local fisherman suggested that the decline in the shellfish harvest may also be due to the practice of laver treatment in the tidal flats of the Ariake Sea. We carried out field and laboratory investigations to determine whether the practice changes the geoenvironmental properties of the fine-grained sediments in the tidal flats. There were notable changes in the salt concentration, pH, and sulfide content between the sediments exposed to a laver treating agent and those without laver treatment. Based on these differences, we identified potential mechanisms by which the laver treating agent was transported into the sediments and influenced the sulfide levels.

We determined the concentrations of 12 endocrine disrupting chemicals (EDCs) in sewage effluents collected from three different sewage treatment plants (STPs) in Hong Kong, and found 4-nonylphenol (NP) and bisphenol A (BPA) were the most abundant EDCs. Effluent concentrations of NP and BPA were higher in dry season than in wet season, but opposite seasonal changes of NP were observed in receiving waters, probably due to the surface runoff. The two secondary STPs showed higher removal efficiency for these compounds than the preliminary STP, while having higher removal efficiency in wet season. Therefore, it is necessary to upgrade the preliminary STP and improve the EDC removal efficiency in dry season. Seawaters from the Cape D’ Aguilar Marine Reserve adjacent to these STPs also exhibited elevated NP levels with a hazard quotient >1. Furthermore, diluted effluents from the STPs elicited significant transcriptional responses of EDC-related genes in the marine medaka fish.

Surface sediments collected from 2001 to 2011 were analyzed for total petroleum hydrocarbons (TPH) and five heavy metals. The sediment concentration ranges of TPH, Zn, Cu, Pb, Cd and Hg were 6.3–535μg/g, 58–332μg/g, 7.2–63μg/g, 4.3–138μg/g, 0–0.98μg/g, and 0.10–0.68μg/g, respectively. These results met the highest marine sediment quality standards in China, indicating that the sediment was fairly clean. However, based on the effects range-median (ERM) quotient method, the calculated values for all of the sampling sites were higher than 0.10, suggesting that there was a potential adverse biological risk in Bohai Bay. According to the calculated results, the biological risk decreased from 2001 to 2007 and increased afterwards. High-risk sites were mainly distributed along the coast. This study suggests that anthropogenic influences might be responsible for the potential risk of adverse biological effects from TPH and heavy metals in Bohai Bay.

Environmental awareness and technological advances has spurred development of new monitoring solutions for the petroleum industry.This paper presents experience from a monitoring program off Norway. To maintain operation within the limits of the government regulations Statoil tested a new monitoring concept. Multisensory data were cabled to surface buoys and transmitted to land via wireless communication. The system collected information about distribution of the drilling wastes and the welfare of the corals in relation to threshold values.The project experienced a series of failures, but the backup monitoring provided information to fulfil the requirements of the permit. The experience demonstrated the need for real time monitoring and how such systems enhance understanding of impacts on marine organisms. Also, drilling operations may improve by taking environmental information into account. The paper proposes to standardize and streamline monitoring protocols to maintain comparability during all phases of the operation and between drill sites.

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy).This article has been retracted at the request of the Editor-in-Chief and the Authors.This paper has to be retracted as the authors have noticed a procedural error with regards to their data which affects the results and discussion of the paper. It is important to note that this is not considered to be the result of scientific misconduct, but rather honest errors by the authors.

Polycyclic aromatic hydrocarbons (PAHs) are emitted into the atmosphere from combustion of fuels, such as emissions from traffic in urban areas, which on their terms can be important sources for the translocation of these toxic compounds to the surrounding region. Pine needles can be used as time–integrated passive air–samplers for PAHs. Pine needles were collected between 2009 and 2011 along a spatial gradient (5km) from urban background sites towards sites situated in a natural park (Collserola) within the metropolitan area of Barcelona. City samples showed PAH levels that were two times higher than the levels in the natural park. A seasonal trend was reflected by the substantially higher PAH levels in pine needles collected in the colder sampling period than those collected in the warmer period. The observed trend can be explained in terms of source emission strength, dilution and photo–chemical degradation, while also gas–pine needles partitioning may have played an important role. The city is the major source area for the translocation of PAHs towards the nearby natural park.

A new salt resistant alkaline phosphatase from eggs of the sea urchin Strongylocentrotus intermedius (StAP) has been shown to have a unique property to hydrolyze substrate in seawater without loss of enzymatic activity. The enzyme has pH optimum at 8.0–8.5. Model experiments showed various concentrations of copper, zinc, cadmium and lead added to seawater or a standard buffer mixture to inhibit completely the enzyme activity at the concentrations of 15–150μg/l. StAP sensitivity to the presence in seawater of metals, pesticides, detergents and oil products appears to be considerably less. Samples of seawater taken from aquatic areas of the Troitsy Bay of the Peter the Great Bay, Japan Sea have been shown to inhibit the enzyme activity; the same was shown for the samples of fresh waters. The phosphatase inhibition assay developed proved to be highly sensitive, technically easy-to use allowing to test a great number of samples.

Fish hold effluent and the effluent produced from the cleaning of fish holds may contain organic material resulting from the degradation of seafood and cleaning products (e.g., soaps and detergents). This effluent is often discharged by vessels into near shore waters and, therefore, could have the potential to contribute to water pollution in bays and estuaries. We characterized effluent from commercial fishing vessels with holds containing refrigerated seawater, ice slurry, or chipped ice. Concentrations of trace heavy metals, wet chemistry parameters, and nutrients in effluent were compared to screening benchmarks to determine if there is a reasonable potential for effluent discharge to contribute to nonattainment of water quality standards. Most analytes (67%) exceeded their benchmark concentration and, therefore, may have the potential to pose risk to human health or the environment if discharges are in significant quantities or there are many vessels discharging in the same areas.