Biofluorescence as a survey tool for cryptic marine species

As ecosystems come under increasing anthropogenic pressure, rare species face the highest risk of extinction. Paradoxically, data necessary to evaluate the conservation status of rare species are often lacking because of the challenges of detecting species with low abundance. One group of fishes subject to this undersampling bias are those with cryptic body patterns. Twenty‐one percent of cryptic fish species assessed for their extinction risk (International Union for Conservation of Nature [IUCN]) are data deficient. We developed a nondestructive method for surveying cryptically patterned marine fishes based on the presence of biofluorescence (underwater biofluorescence census, UBC). Blue LED torches were used to investigate how widespread biofluorescence was in cryptic reef fishes in the Coral Triangle region. The effectiveness of UBC to generate abundance data was tested on a data‐deficient pygmy seahorse species (Hippocampus bargibanti) and compared with data obtained from standard underwater visual census (UVC) surveys. We recorded 95 reef fish species displaying biofluorescence, 73 of which had not been previously described as biofluorescent. Of those fish with cryptic patterns, 87% were biofluorescent compared with 9% for noncryptic fishes. The probability of species displaying biofluorescence was 70.9 times greater for cryptic species than for noncryptic species. Almost twice the number of H. bargibanti was counted using the UBC compared with UVC. For 2 triplefin species (Ucla xenogrammus, Enneapterygius tutuilae), the abundance detected with UBC was triple that detected with UVC. The UBC method was effective at finding cryptic species that would otherwise be difficult to detect and thus will reduce interobserver variability inherent to UVC surveys. Biofluorescence is ubiquitous in cryptic fishes, making this method applicable across a wide range of species. Data collected using UBC could be used with multiple IUCN criteria to assess the extinction risk of cryptic species. Adopting this technique will enhance researchers’ ability to survey cryptic species and facilitate management and conservation of cryptic marine species.     

European Atlas of the Seas: “a picture is worth a thousand words”

The European Atlas of the Seas offers a snapshot of environmental and socio-economic features that characterize the coastal and marine environment. The latest release (Version 4) addresses the public in general, but also non-specialist experts involved with environmental issues, human activities or policies related to Europe’s coasts and seas. The information content of the Atlas comprises a series of geographical layers, subdivided in “background maps”, “thematic maps” (i.e. maritime Europe, natural setting, sea bottom, sea level rise, security, transport, tourism, energy, wind, fisheries and fish consumption) and “do-it-yourself maps” (dealing with marine knowledge, nature and environment, socio-economics, fisheries, aquaculture, transport, energy, sea bed mining, coastal tourism, Maritime Spatial Planning, integrated maritime surveillance, and international ocean governance). All maps follow consistent cartographic rules and can be extracted for external use. The Atlas database is updated regularly, but historical data remain accessible after the updates, so that time series may be constructed. Tools for map exploration and combination can be used to combine together more layers, providing professional users with analysis and interpretation capabilities, to couple data into graphical indicators. The Atlas aims to supports also policy making, on marine environment, maritime issues and economic sectors, both within and outside the European Institutions (e.g. on Common Fisheries Policy or Maritime Spatial Planning). Further, it expands the same support to near-coastal issues and matters related to land-sea interactions. The web application for accessing Atlas contents offers links to other Marine Information Systems, and is available to a broad audience from computers, tablets and mobile devices.     

Comparison of DNA extraction methodologies used for assessing fungal diversity via ITS sequencing

Traditional methods of assessing fungal exposure have been confounded by a number of limiting variables. The recent utilization of molecular methods such as internal transcribed spacer (ITS) sequencing of ribosomal RNA genes has provided improved insight into the diversity of fungal bioaerosols in indoor, outdoor and occupational environments. However, ITS analyses may also be confounded by a number of methodological limitations. In this study, we have optimized this technology for use in occupational or environmental studies. Three commonly used DNA extraction methodologies (UltraClean Soil kit, High Pure PCR Template kit, and EluQuik/DNeasy kit) were compared in terms of sensitivity and susceptibility to PCR inhibitors in dust for three common fungal bioaerosols, Aspergillus versicolor, Rhizopus microsporus and Wallemia sebi. Environmental dust samples were then studied using each extraction methodology and results were compared to viable culture data. The extraction methods differed in terms of their ability to efficiently extract DNA from particular species of fungi (e.g. Aspergillus versicolor). In addition, the ability to remove PCR inhibitors from dust samples was most effective using the soil DNA extraction kit. The species composition varied greatly between ITS clone libraries generated with the different DNA extraction kits. However, compared to viable culture data, ITS clone libraries included additional fungal species that are incapable of growth on solid culture medium. Collectively, our data indicated that DNA extraction methodologies used in ITS sequencing studies of occupational or environmental dust samples can greatly influence the fungal species that are detected.     

Triphenyltin alters lipid homeostasis in females of the ramshorn snail Marisa cornuarietis

Molluscs are sensitive species to the toxic effects of organotin compounds, particularly to masculinisation. Both tributyltin (TBT) and triphenyltin (TPT) have been recently shown to bind to mollusc retinoid X receptor (RXR). If RXR is involved in lipid homeostasis, exposure to TPT would have an immediate effect on endogenous lipids. To test this hypothesis, the ramshorn snail Marisa cornuarietis was exposed to environmentally relevant concentrations of TPT (30, 125, 500 ng/L as Sn) in a semi-static water regime for 7 days. Percentage of lipids and total fatty acid content decreased significantly in TPT-exposed females while the activity of peroxisomal acyl-CoA oxidase, involved in fatty acid catabolism, increased. In addition, fatty acid profiles (carbon chain length and unsaturation degree) were significantly altered in exposed females but not in males. This work highlights the ability of TPT to disrupt lipid metabolism in M. cornuarietis at environmentally realistic concentrations and the higher susceptibility of females in comparison to males.     

Airborne trace element pollution in 11 European cities assessed by exposure of standardised ryegrass cultures

Within a European biomonitoring programme, Italian ryegrass (Lolium multiflorum Lam.) was employed as accumulative bioindicator of airborne trace elements (As, Cd, Cr, Cu, Fe, Ni, Pb, Sb, V, Zn) in urban agglomerations. Applying a highly standardised method, grass cultures were exposed for consecutive periods of four weeks each to ambient air at up to 100 sites in 11 cities during 2000–2002. Results of the 2001 exposure experiments revealed a clear differentiation of trace element pollution within and among local monitoring networks. Pollution was influenced particularly by traffic emissions. Especially Sb, Pb, Cr, Fe, and Cu exhibited a very uneven distribution within the municipal areas with strong accumulation in plants from traffic-exposed sites in the city centres and close to major roads, and moderate to low levels in plants exposed at suburban or rural sites. Accumulation of Ni and V was influenced by other emission sources. The biomonitoring sites located in Spanish city centres featured a much higher pollution load by trace elements than those in other cities of the network, confirming previously reported findings obtained by chemical analyses of dust deposition and aerosols. At some heavily-trafficked sites, legal thresholds for Cu, Pb, and V contents in foodstuff and animal feed were reached or even surpassed. The study confirmed that the standardised grass exposure is a useful and reliable tool to monitor and to assess environmental levels of potentially toxic compounds of particulate matter.     

Degradation of explosives-related compounds using nickel catalysts

We report the ability of nickel-based catalysts to degrade explosives compounds in aqueous solution. Several nickel catalysts completely degraded the explosives, although rates varied. Nearly all of the organic explosive compounds tested, including 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), were rapidly degraded to below detection limits by a powdered nickel on an alumina-silicate support (Aldrich nickel catalyst). Perchlorate degradation was minimal (<25%). Degradation of TNT by Aldrich nickel catalyst resulted in apparent first-order kinetics. Significant gaseous 14C was released and collected in an alkaline solution (most likely carbon dioxide) from [14C]RDX and [14C]HMX, indicating heterocyclic ring cleavage. Significant gaseous 14C was not produced from [14C]TNT, but spectrophotometric evidence indicated loss of aromaticity. Degradation occurred in low ionic strength solutions, groundwater, and from pH 3 to pH 9. Degradation of TNT, RDX, and HMX was maintained in flow-through columns of Aldrich nickel catalyst mixed with sand down to a hydraulic retention time of 4h. These data indicate that nickel-based catalysts may be an effective means for remediation of energetics-contaminated groundwater.     

Alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil

For 503 days, unoiled control and artificially oiled sediments were incubated in situ at 20m water depth in a Mediterranean coastal area. Degradation of the aliphatic fraction of the oil added was followed by GC-MS. At the same time, terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA encoding genes was used to detect dynamics in the sulfate-reducing bacteria (SRB) community in response to the oil contamination. Specific polymerase chain reaction (PCR) primer sets for five generic or suprageneric groups of SRB were used for PCR amplification of DNA extracted from sediments. During the experiment, hydrocarbons from C(17) to C(30) were significantly degraded even in strictly anoxic sediment layers. Of the five SRB groups, only two groups were detected in the sediments (control and oiled), namely the Desulfococcus-Desulfonema-Desulfosarcina-like group and the Desulfovibrio-Desulfomicrobium-like group. Statistical analysis of community patterns revealed dynamic changes over time within these two groups following the contamination. Significant differences in community patterns were recorded in artificially oiled compared with control sediments. Cloning and sequencing of 16S rRNA encoding genes performed after 503 days showed that many of the most abundant sequences were closely related to hydrocarbonoclastic SRB which could have played an active role in the observed biodegradation of aliphatic hydrocarbons. Results from the present study provide useful information on the dynamics of dominant SRB in heavily oil-contaminated sediments and their potential for anaerobic biodegradation for the treatment of spilled oil in anoxic marine environments.     

Corrosion and stability study of Bacillus thuringiensis var. kurstaki starch industry wastewater-derived biopesticide formulation

Biopesticides are usually sprayed on forests by using planes made up of aluminum alloy. Bioval derived from starch industry wastewater (SIW) in suspension form was developed as stable anticorrosive biopesticide formulation. In this context, various anticorrosion agents such as activated charcoal, glycerin, ethylene glycol, phytic acid, castor oil and potassium silicate were tested as anticorrosive agents. There was no corrosion found in Bioval formulation where potassium silicate (0.5% w/v) was added and compared with Foray 76 B, as an industrial standard, when stored over 6 months. In relation to other parameters, the anticorrosion formulation of Bioval+buffer+KSi reported excellent zeta potential (?33.19 ± 4 mV) and the viscosity (319.13 ± 32 mPa.s) proving it's stability over 6 months, compared to the standard biopesticide Foray 76 B (?36.62 ± 4 mV potential zeta, pH 4.14 ± 0.1 and 206 ± 21 mPa.s viscosity). Metal analysis of the different biopesticides showed that Bioval+buffer+KSi has no corrosion (5.11 ± 0.5 mg kg^?1 of Al and 13.53 ± 1.5 mg kg^?1 of Fe) on the aluminum alloy due to the contribution of sodium acetate buffer at pH 5. The bioassays reported excellent results for Bioval+Buffer+KSi (2.95 ± 0.3 × 10⁹ CFU mL^?1 spores and 26.6 ± 2.7 × 10⁹ IU L^?1 Tx) compared with initial Bioval (2.46 ± 0.3 × 10⁹ CFU mL^?1 spores and 23.09 ± 3 × 10⁹ IU L^?1 Tx) and Foray 76 B (2.3 ± 0.2 × 10⁹ CFU mL^?1 spores and 19.950 ± 2.1 UI L^?1 Tx) which was due to the break-up of the external chitinous membrane due to abrasive action of potassium silicate after ingestion by insects. The contribution of sodium acetate buffer and potassium silicate (0.5% and at pH = 5) as anticorrosion agent in the Bioval allowed production of an efficient biopesticide with a reduced viscosity and favorable pH as compared to Foray 76 B which enhanced the entomotoxic potential against spruce budworm (SB) larvae (Lepidoptera: Choristoneura fumiferana).     

Pedogenesis and nickel biogeochemistry in a typical Albanian ultramafic toposequence

This study aimed at relating the variability of Ni biogeochemistry along the ultramafic toposequence to pedogenesis and soil mineralogy. Hypereutric Cambisols dominate upslope; Cambic Vertisols and Fluvic Cambisols occur downslope. The soil mineralogy showed abundance of primary serpentine all over the sequence. It is predominant upslope but secondary smectites dominate in the Vertisols. Free Fe-oxides are abundant in all soils but slightly more abundant in the upslope soils. Whereas serpentines hold Ni in a similar and restricted range in every soil (approx. 0.3 %), Ni contents in smectites may vary a lot and Mg-rich and Al-poor smectites in the Vertisol could hold up to 4.9 % Ni. Ni was probably adsorbed onto amorphous Fe-oxides and was also exchangeable in secondary smectites. High availability of Ni in soils was confirmed by DTPA extractions. However, it varied significantly along the toposequence, being higher in upslope soils, where Ni-bearing amorphous Fe-oxides were abundant and total organic carbon higher and sensibly lower downslope on the Vertisols: Ni_DTPA varied from 285 mg kg^?1 in the surface of soil I (upslope) to 95.9 mg kg^?1 in the surface of Fluvic Cambisols. Concentration of Ni in Alyssum murale shoots varied from 0.7 % (Hypereutric Cambisols) to 1.4 % (Hypereutric Vertisol). Amazingly, Ni uptake by A. murale was not correlated to Ni_DTPA, suggesting the existence of specific edaphic conditions that affect the ecophysiology of A. murale upslope.     

Copper and cadmium effects on growth and extracellular exudation of the marine toxic dinoflagellate Alexandrium catenella: 3D-fluorescence spectroscopy approach

In this study, metal contamination experiments were conducted to investigate the effects of copper and cadmium on the growth of the marine toxic dinoflagellate Alexandrium catenella and on the production of dissolved organic matter (Dissolved Organic Carbon: DOC; Fluorescent Dissolved Organic Matter: FDOM). This species was exposed to increasing concentrations of Cu²⁺ (9.93 × 10⁻¹⁰–1.00 × 10⁻⁷ M) or Cd²⁺ (1.30 × 10⁻⁸–4.38 × 10⁻⁷ M), to simulate polluted environments. The drastic effects were observed at pCu²⁺ = 7.96 (Cu²⁺: 1.08 × 10⁻⁸ M) and pCd²⁺ = 7.28 (Cd²⁺: 5.19 × 10⁻⁸ M), where cyst formation occurred. Lower levels of Cu²⁺ (pCu²⁺ > 9.00) and Cd²⁺ (pCd²⁺ > 7.28) had no effect on growth. However, when levels of Cu²⁺ and Cd²⁺ were beyond 10⁻⁷ M, the growth was totally inhibited. The DOC released per cell (DOC/Cell) was different depending on the exposure time and the metal contamination, with higher DOC/Cell values in response to Cu²⁺ and Cd²⁺, comparatively to the control. Samples were also analyzed by 3D-fluorescence spectroscopy, using the Parallel Factor Analysis (PARAFAC) algorithm to characterize the FDOM. The PARAFAC analytical treatment revealed four components (C1, C2, C3 and C4) that could be associated with two contributions: one, related to the biological activity; the other, linked to the decomposition of organic matter. The C1 component combined a tryptophan peak and a characteristic humic substances response, and the C2 component was considered as a tryptophan protein fluorophore. The C3 and C4 components were associated to marine organic matter production.