This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters.

Embryo toxicity of particles generated by combustion processes is of special concern for human health. A significant part of these toxic effects is linked to the binding of some pollutants (like polycyclic aromatic hydrocarbons or PAHs) to the Aryl hydrocarbon Receptor (AhR) and the activation of target genes, like the cytochrome P4501A. This activity was analyzed for ambient air and coal-combustion particle extracts in zebrafish embryos (the cyp1aDarT assay) and in two single-cell bioassays: the yeast-based YCM-RYA and the DR-luc (rat cells) assay. Observed AhR ligand activity of samples generally correlated to the predicted toxic effect according to their PAH composition, except for one of the coal combustion samples with an anomalously high activity in the cyp1aDarT assay. This sample induced deformities in zebrafish embryos. We concluded that the combination of morphological and molecular assays may detect embryonic toxic effects that cannot be predicted from chemical analyses or single-cell bioassays.

We tested the hypothesis that the biodegradation of volatile petroleum hydrocarbons (VPHs) in aerobic sandy soil is affected by the blending with 10 percent ethanol (E10) or 20 percent biodiesel (B20). When inorganic nutrients were scarce, competition between biofuel and VPH degraders temporarily slowed monoaromatic hydrocarbon degradation. Ethanol had a bigger impact than biodiesel, reflecting the relative ease of ethanol compared to methyl ester biodegradation. Denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA genes revealed that each fuel mixture selected for a distinct bacterial community, each dominated by Pseudomonas spp. Despite lasting impacts on soil bacterial ecology, the overall effects on VHP biodegradation were minor, and average biomass yields were comparable between fuel types, ranging from 0.40 ± 0.16 to 0.51 ± 0.22 g of biomass carbon per gram of fuel carbon degraded. Inorganic nutrient availability had a greater impact on petroleum hydrocarbon biodegradation than fuel composition.

To understand the role of abundance of tfdA gene classes belonging to β- and γ-proteobacteria on phenoxy acid herbicide degradation, streambed sediments were sampled around three seepage meters (SMs) installed in a landfill-impacted groundwater–surface water interface. Highest herbicide mass discharge to SM3, and lower herbicide mass discharges to SM1 and SM2 were determined due to groundwater discharge rates and herbicide concentrations. SM1-sediment with the lowest abundance of tfdA gene classes had the slowest mineralization, whereas SM2- and SM3-sediments with more abundant tfdA genes had faster mineralization. The observed difference in mineralization rates between discharge zones was simulated by a Monod-based kinetic model, which confirmed the role of abundance of tfdA gene classes. This study suggests presence of specific degraders adapted to slow growth rate and high yield strategy due to long-term herbicide exposure; and thus groundwater–surface water interface could act as a natural biological filter and protect stream water quality.

Short-term changes in levels of expression of nine stress response genes and oxidative damage of proteins were examined in Eisenia fetida exposed to polyvinylpyrrolidone (PVP) coated Ag nanoparticles (Ag-NP) and AgNO₃ in natural soils. The responses varied significantly among days with the highest number of significant changes occurring on day three. Similarity in gene expression patterns between Ag-NPs and AgNO₃ and significant relationships of expression of CAT and HSP70 with Ag soil concentration suggest similarity in toxicity mechanisms of Ag ions and NPs. Significant increases in the levels of protein carbonyls on day three of the exposure to both ions and Ag-NPs indicate that both treatments induced oxidative stress. Our results suggest that Ag ions drive short term toxicity of Ag-NPs in E. fetida. However, given that <15% of Ag in the NPs was oxidized in these soils, dissolution of Ag-NPs is likely to occur after or during their uptake.

There is growing concern over the potential detrimental impact of ionizing radiation on natural biota. The mechanistic cause-and-effect impact of ionizing radiation has yet to be characterized in any aquatic species. Adopting an integrated approach, including radiochemical analysis of environmental samples, we evaluate molecular responses to ionizing radiation in the marine mussel, Mytilus edulis. These responses included analyses of RAD51 mRNA expression, a gene involved in the repair of DNA double strand breaks, and induction of DNA strand breaks using the comet assay, in samples collected from a site impacted by low level ionizing radiation discharges. Based on activities of the radionuclides measured in sediment and mussel tissue at the discharge site, external and internal dose rates were low, at ca. 0.61 μGyh⁻¹ and significantly lower than the generic (all species) “no effect” dose rate of 10 uGyh⁻¹, yet DNA strand breakage and RAD51 mRNA expression were both altered.

This study is a first attempt to investigate the impact of urban contamination on metal tolerance of heterotrophic river biofilms using a short-term test based on β-glucosidase activity. Tolerance levels to Cu, Cd, Zn, Ni and Pb were evaluated for biofilms collected at three sites along an urban gradient in the Seine river (France). Metallic pollution increased along the river, but concentrations remained low compared to environmental quality standards. Biofilm metal tolerance increased downstream from the urban area. Multivariate analysis confirmed the correlation between tolerance and contamination and between multi-metallic and physico-chemical gradients. Therefore, tolerance levels have to be interpreted in relation to the whole chemical and physical characteristics and not solely metal exposure. We conclude that community tolerance is a sensitive biological response to urban pressure and that mixtures of contaminants at levels lower than quality standards might have a significant impact on periphytic communities.

Tropical coastal ecosystems, such as mangroves, have a great ecological and socioeconomic importance for adjacent systems and local populations, but intensive environmental impact monitoring is still lacking, mainly in East Africa. This study evaluated the potential anthropogenic disturbance on Palaemon concinnus population structure and fitness. Palaemon concinnus populations from one peri-urban (domestic sewage impacted) and two pristine mangrove creeks were studied by sampling nearly 100 shrimps per location every 15 days for 12 months. The shrimps at the peri-urban location were larger, experienced longer reproductive periods, presented higher proportion of ovigerous females and better embryo quality when compared with shrimps inhabiting pristine locations. Physiological indices (RNA/DNA ratio) were similar between shrimps at pristine and peri-urban mangroves. However, a higher level of parasitation by a Bopyridae isopod, Pseudione elongata indicated some degree of stress on the host at the peri-urban mangrove, with potential effects on the host population dynamics.

A phenanthrene-degrading bacterium, Sphingomonas paucimobilis EPA505 was used to construct two fluorescence-based reporter strains. Strain D harboring gfp gene was constructed to generate green fluorescence when the strain started to biodegrade phenanthrene. Strain S possessing gef gene was designed to die once phenanthrene biodegradation was initiated and thus to lose green fluorescence when visualized by a live/dead cell staining. Confocal laser scanning microscopic observation followed by image analysis demonstrates that the fluorescence intensity generated by strain D increased and the intensity by strain S decreased linearly at the phenanthrene concentration of up to 200 mg/L. Such quantitative increase and decrease of fluorescence intensity in strain D (i.e., from 1 to 11.90 ± 0.72) and strain S (from 1 to 0.40 ± 0.07) were also evident in the presence of Ottawa sand spiked with the phenanthrene up to 1000 mg/kg. The potential use of the reporter strains in quantitatively determining biodegradable or toxic phenanthrene was discussed.