High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems.

Environmental diversity surveys are crucial for the bioassessment of anthropogenic impacts on marine ecosystems. Traditional benthic monitoring relying on morphotaxonomic inventories of macrofaunal communities is expensive, time-consuming and expertise-demanding. High-throughput sequencing of environmental DNA barcodes (metabarcoding) offers an alternative to describe biological communities. However, whether the metabarcoding approach meets the quality standards of benthic monitoring remains to be tested. Here, we compared morphological and eDNA/RNA-based inventories of metazoans from samples collected at 10 stations around a fish farm in Scotland, including near-cage and distant zones. For each of 5 replicate samples per station, we sequenced the V4 region of the 18S rRNA gene using the Illumina technology. After filtering, we obtained 841,766 metazoan sequences clustered in 163 Operational Taxonomic Units (OTUs). We assigned the OTUs by combining local BLAST searches with phylogenetic analyses. We calculated two commonly used indices: the Infaunal Trophic Index and the AZTI Marine Biotic Index. We found that the molecular data faithfully reflect the morphology-based indices and provides an equivalent assessment of the impact associated with fish farms activities. We advocate that future benthic monitoring should integrate metabarcoding as a rapid and accurate tool for the evaluation of the quality of marine benthic ecosystems.

Unlocking nature's treasure-chest: screening for oleaginous algae.

Micro-algae synthesize high levels of lipids, carbohydrates and proteins photoautotrophically, thus attracting considerable interest for the biotechnological production of fuels, environmental remediation, functional foods and nutraceuticals. Currently, only a few micro-algae species are grown commercially at large-scale, primarily for "health-foods" and pigments. For a range of potential products (fuel to pharma), high lipid productivity strains are required to mitigate the economic costs of mass culture. Here we present a screen concentrating on marine micro-algal strains, which if suitable for scale-up would minimise competition with agriculture for water. Mass-Spectrophotometric analysis (MS) of nitrogen (N) and carbon (C) was subsequently validated by measurement of total fatty acids (TFA) by Gas-Chromatography (GC). This identified a rapid and accurate screening strategy based on elemental analysis. The screen identified Nannochloropsis oceanica CCAP 849/10 and a marine isolate of Chlorella vulgaris CCAP 211/21A as the best lipid producers. Analysis of C, N, protein, carbohydrate and Fatty Acid (FA) composition identified a suite of strains for further biotechnological applications e.g. Dunaliella polymorpha CCAP 19/14, significantly the most productive for carbohydrates, and Cyclotella cryptica CCAP 1070/2, with utility for EPA production and N-assimilation.

Ecological impacts of large-scale disposal of mining waste in the deep sea.

Deep-Sea Tailings Placement (DSTP) from terrestrial mines is one of several large-scale industrial activities now taking place in the deep sea. The scale and persistence of its impacts on seabed biota are unknown. We sampled around the Lihir and Misima island mines in Papua New Guinea to measure the impacts of ongoing DSTP and assess the state of benthic infaunal communities after its conclusion. At Lihir, where DSTP has operated continuously since 1996, abundance of sediment infauna was substantially reduced across the sampled depth range (800-2020 m), accompanied by changes in higher-taxon community structure, in comparison with unimpacted reference stations. At Misima, where DSTP took place for 15 years, ending in 2004, effects on community composition persisted 3.5 years after its conclusion. Active tailings deposition has severe impacts on deep-sea infaunal communities and these impacts are detectable at a coarse level of taxonomic resolution.

Comparison of screening methods for high-throughput determination of oil yields in micro-algal biofuel strains.

The phenotypic and phylogenetic diversity of micro-algae capable of accumulating triacylglycerols provides a challenge for the accurate determination of biotechnological potential. High-yielding strains are needed to improve economic viability and their compositional information is required for optimizing biodiesel properties. To facilitate a high-throughput screening programme, a very rapid direct-derivatization procedure capable of extracting lyophilized material for GC analysis was compared with a scaled-down Folch-based method. This was carried out on ten micro-algal strains from 6 phyla where the more rapid direct-derivatization approach was found to provide a more reliable measure of yield. The modified Folch-based procedure was found to substantially underestimate oil yield in one Chlorella species (P < 0.01). In terms of fatty acid composition however, the Folch procedure proved to be slightly better in recovering polyunsaturated fatty acids, in six out of the ten strains. Therefore, direct-derivatization is recommended for rapid determination of yields in screening approaches but can provide slightly less compositional accuracy than solvent-based extraction methods.

Metals and other elements in tissues of wild fish from fish farms and comparison with farmed species in sites with oxic and anoxic sediments.

Farmed fish and wild fish aggregating in the vicinity of four Mediterranean fish farms with different environmental conditions were sampled. Levels of metals (including As and Se) were measured in the muscle, liver, gills, bone and intestine. The wild fish from sites with anoxic substrata accumulate metals (including As and Se) from the ambient habitat in their gills whereas those from sites with oxic substrata concentrate these elements through their diet in their intestine. Tissues of wild fish aggregating around farm cages accumulate a greater number of these elements and with higher concentrations than farmed fish. Habitat, diet, ecological needs, fat content of fish, and protein expression may play an important role in these element differences between fish species. Fe in flathead grey mullet, As in surmullet, rainbow wrasse, grey gurnard and picarel and Hg in bogue may pose a risk for human health. Farmed and wild fish are good sources of P, K, Cr and Se while flathead grey mullet, picarel and comber are excellent sources of Ca and Se.

Biogas from Macroalgae: is it time to revisit the idea?

The economic and environmental viability of dedicated terrestrial energy crops is in doubt. The production of large scale biomass (macroalgae) for biofuels in the marine environment was first tested in the late 1960's. The culture attempts failed due to the engineering challenges of farming offshore. However the energy conversion via anaerobic digestion was successful as the biochemical composition of macroalgae makes it an ideal feedstock. The technology for the mass production of macroalgae has developed principally in China and Asia over the last 50 years to such a degree that it is now the single largest product of aquaculture. There has also been significant technology transfer and macroalgal cultivation is now well tried and tested in Europe and America. The inherent advantage of production of biofuel feedstock in the marine environment is that it does not compete with food production for land or fresh water. Here we revisit the idea of the large scale cultivation of macroalgae at sea for subsequent anaerobic digestion to produce biogas as a source of renewable energy, using a European case study as an example.

A new generation of biocides for control of crustacea in fish farms.

Farming of salmon has become a significant industry in many countries over the past two decades. A major challenge facing this sector is infestation of the salmon by sea lice. The main way of treating salmon for such infestations is the use of medicines such as organophosphates, pyrethrins, hydrogen peroxide or benzoylphenyl ureas. The use of these medicines in fish farms is, however, highly regulated due to concerns about contamination of the wider marine environment. In this paper we report the use of photochemically active biocides for the treatment of a marine copepod, which is a model of parasitic sea lice. Photochemical activation and subsequent photodegradation of PDAs may represent a controllable and environmentally benign option for control of these parasites or other pest organisms in aquaculture.

Antioxidant modulation of oxidant-stimulated uptake and release of arachidonic acid in eicosapentaenoic acid-supplemented human lymphoma U937 cells.

Omega-3 polyunsaturated fatty acids (PUFA) are increasingly finding use as treatments for a variety of medical conditions. PUFA supplementation can, however, result in increased oxidative stress causing elevated turnover rate of membrane phospholipids, impairment of membrane integrity and increased formation of inflammatory mediators. The aim of this study was to determine which antioxidant compounds were most effective in ameliorating the stimulation of phospholipid turnover by oxidative stress. U937 cells were supplemented with eicosapentaenoic acid and either ascorbic acid, alpha-tocopherol, beta-carotene or astaxanthin prior to being challenged with oxidant. Although all antioxidants were found to be effective in decreasing oxidant-stimulated peroxide formation, only alpha-tocopherol significantly decreased oxidant-stimulated release of 3H-labeled arachidonic acid (AA), while ascorbic acid markedly increased release. All antioxidants except alpha-tocopherol decreased oxidant-stimulated 3H-AA uptake. Our data suggest that antioxidants are not equally effective in combating the effects of oxidative stress upon membrane phospholipid turnover, and that optimal protection will require mixtures of antioxidants.

Copper, zinc and cadmium in marine cage fish farm sediments: an extensive survey.

The diet of cage-farmed Atlantic salmon contains a range of trace metals, some of which have toxic properties, e.g. zinc, copper and cadmium. A survey of metal concentrations (ICP-MS analysis) in surface sediments of ca. 70 stations was carried out in both May and December 2000 around a Scottish fish farm. Additionally, at 13 stations on 2 orthogonal transects centered on the farm, sediments were analysed at 1cm intervals to 8 cm depth. Maximum concentrations in surface sediments were 921, 805 and 3.5 microg g(-1) for Zn, Cu and Cd, respectively, and were found at stations near the fish farm. The calculated losses from the farm (feed input minus fish output) were 87.0%, 4.3% and 14.0% of the background-corrected inventories for Zn, Cu and Cd, respectively, indicating that for Cu and Cd at least, the feed is not the only source.

Differential effects of eicosapentaenoic and docosahexaenoic acids upon oxidant-stimulated release and uptake of arachidonic acid in human lymphoma U937 cells.

The use of n-3 polyunsaturated fatty acids, as found in fish-oil derived dietary supplements, as anti-inflammatory agents is supported by a variety of biochemical and physiological data. Recent studies investigating the therapeutic potential of long chain (>C20) n-3 fatty acids in mental illness have lead to the conclusion, however, that not all n-3 fatty acid types are equally efficacious. In particular eicosapentaeoic acid (EPA) appears to possess antidepressant and antipsychotic activity, while docosahexaenoic acid (DHA) does not, an effect suggested to be due to a differential ability to antagonize arachidonic acid (AA)-dependent cell signalling. In this study, we examine the effect of EPA and DHA supplementation upon uptake and release of arachidonic acid stimulated by tert-butyl hydroperoxide/Fe2+ in U937 cells. Oxidant-stimulated 3H-AA release from cells was enhanced by pre-treatment with EPA, DHA and AA, but not stearic or oleic acids for 18 days, with the order of effect magnitude being EPA > DHA = AA. Supplementation of cells for 1 day gave qualitatively similar results, although the effect magnitude was smaller. To determine whether enhanced release was due to decreased reuptake of AA, cells were cultured in the presence of 10 microM fatty acids. Pre-treatment of cells with EPA, and to a lesser extent AA, but not DHA, inhibited uptake of 3H-AA measured subsequent to the removal of unesterified fatty acids. This study suggests that, in U937 cells, EPA can alter the rate of uptake and release of AA from phospholipids in an exposure time-dependent manner, whereas DHA has no or little effect. Our results predict that EPA will have a more pronounced effect upon AA-dependent processes compared to DHA, and suggests that the relative amounts of EPA and DHA in fish oil supplements may modify their biochemical, and potentially, behavioural effects.