Quantitative PCR to estimate copepod feeding

Copepods play a central role in marine food webs as grazers of plankton and as key prey for many predators. Therefore, quantifying their specific trophic interactions is critical for understanding the role of copepods in ocean processes. However, because of methodological constraints, it remains difficult to investigate in situ copepod feeding without reliance on laborious intrusive and potentially biased incubation approaches. Recent advances in PCR-based methodologies have demonstrated the feasibility of directly identifying copepod diets based on prey DNA sequences. Yet, obtaining quantitative information from these approaches remains challenging. This study presents results of systematic efforts to develop a quantitative PCR (qPCR) assay targeted to 18S rRNA gene fragments to estimate copepod gut content of specific species of prey algae. These results were first compared to gut content estimates based on fluorescence in the copepod Calanus finmarchicus fed monocultures of two different microalgae species in controlled laboratory studies. In subsequent field studies, we compared feeding rates obtained by microscopy and qPCR for Temora longicornis and Acartia clausi feeding on the haptophyte Phaeocystis globosa in natural blooms. These investigations demonstrate a semi-quantitative relationship between gut content estimates derived from qPCR, gut pigment, and direct microscopy. However, absolute estimates of gut content based on qPCR methodology were consistently lower than expected. This did not appear to be explained by the extraction methods used, or interference by non-target (predator) DNA in the PCR reactions, instead suggesting digestion of prey-specific nucleic acids. Furthermore, the 18S rDNA target gene copy number of the phytoplankton varied with growth phase. Nonetheless, when prey target gene copy number in the ambient water is quantified, the qPCR-approach can be compared to other methods, and then used to semi-quantitatively estimate relative copepod grazing on specific prey in situ without involving further incubations. A distinct advantage of a DNA-based molecular approach compared to gut fluorescence and direct microscopic observation, is the ability to detect non-pigmented and macerated prey. Future studies should aim to correct for breakdown in prey DNA and perform extensive calibrations to other methods in order to achieve a quantitative measure of feeding rates in situ.     

Assessment of the effect of environmental pollution in a marina on caged mussels using chemical and genotoxic analysis

An integrated approach using the contamination levels and DNA damage in mussels (Mytilus galloprovincialis) was applied in order to assess the chemical contamination in a marina (Eastern coastline of Aegean Sea). Mussels, which were harvested from a reference site (Foca), were transplanted into a marina situated along the coast of Izmir Bay. The transplanted mussels were collected at the 14th, 30th and 60th day of the experimental period. Polycyclic aromatic hydrocarbon (PAH) levels (27–51?ng?g^?1?wet?weight) detected in the mussels were similar to the levels detected in other coastal areas of the Mediterranean Sea. The marina’s sediment was found to be contaminated with PAHs (∑PAH?=?25?µg?g^?1) of pyrolytic origin and may become a source of pollution and a threat to the marine environment. In order to assess the DNA damage, the haemolymph and gill cells of the mussels were used for the comet analysis and considered as an indicator of exposure to genotoxic chemicals including 16 PAH compounds and metals. The highest levels of DNA damage expressed as %Tail-DNA (%T-DNA) were observed at the end of the experiment (21.5% T-DNA). The correlation analyses conducted between 2-, 3-, 4-ring PAHs in mussels and %T-DNA in haemolymph and gill cells showed a significant positive correlation. This investigation confirmed that transplanted mussel can be a useful tool to determine PAH contamination in marinas.     

Trace metal distribution in different chemical fractions of marine sediments along the eastern Aegean shelf

The major objective of this study was to carry out sequential chemical extraction for the partitioning of particulate trace metals in sediment samples, collected along the eastern Aegean shelf during cruises July‐August 1994, in the framework of a National Marine Measurement and Monitoring Programme for the Aegean Sea.

Five metals, Cd, Pb, Cu, Zn and Cr were examined in each of sediment samples. Three chemical fractions of the sediments were separated and concentrations of the trace metals were determined by AAS techniques. The three different leaches used were hydroxylamine hydrochloride‐acetic acid, hydrogen peroxide and nitric‐perchloric acids.

Metals were concentrated mainly in the fraction extracted by nitric‐perchloric acids. Lead in the first fraction were found in the sediments of Northern part of Aegean, where the concentration of organic material was high.

The total concentrations of Cd, Cu, Zn, Cr were higher in Izmir Bay than the other sampling points. The distribution of Pb concentrations was the highest in Edremit Bay and Izmir Bay.     

Polycyclic aromatic hydrocarbons in red mullet (Mullus bavbatus) and sediments from the Eastern Aegean Sea

The distribution of polycyclic aromatic hydrocarbons (PAHs) was investigated in red mullet (Mullus barbatus) and sediment samples in the eastern Aegean Sea. The data were collected during cruises in July and November 1994, in the framework of National Marine Measurement and Monitoring Programme in the Aegean Sea. PAHs were detected in the tissue of Mullus barbatus of different sex and size from nine sampling sites throughout the study area ranging from 0.03 to 0.46 ug/g (fresh weight). The observations show the high levels of PAHs were found in tissues of females. The average concentration of PAHs in Aegean Sea sediments ranged from 0.20 to 1.8 ug/g (dry weight). No significant correlation was observed between PAH and sedimentary organic carbon.     

Cytogenetic and epigenetic alterations by cobalt and nickel on Zea mays L

Changes in DNA methylation in Zea mays plantlets in response to cobalt and nickel (5, 10, 20, and 40 mmol L^?1) evaluated by the coupled restriction enzyme digestion-random amplification technique revealed dose-related increases in hypermethylation. The effects on mitotic index and phytohormone levels were also determined. Co and Ni caused a decrease in mitotic index and an attenuation in the growth-promoting hormones gibberellic acid, zeatin, and indole acetic acid, while abscisic acid levels rose. These findings have shown that the increase in abscisic acid levels and DNA methylation depend on the concentrations of Co and Ni.