Laboratoire de Biotechnologie et Chimie Marines

The aim of the present study is to review and tentatively to interpret the optical behavior of oceanic case I waters, those waters for which phytoplankton and their derivative play a predominant role in determining their optical properties. Chlorophyll‐like pigment concentration is used as the index to quantify the algal material (living and detrital), and statistical relationships between this index and the depth of the euphotic layer, the spectral values of the attenuation coefficient for downwelling irradiance, or the scattering coefficient are investigated. On the basis of these statistical relationships a pigment‐dependent optical model is developed. It allows the propagation of the visible radiant energy within the ocean or the backscattered radiation from the upper layer to be predicted as a function of the local phytoplanktonic content. Other geophysical or geochemical applications are derived which concern the heating rate due to penetrating visible radiations or the rate of energy storage due to photosynthesis. The nonlinear trends observed in the algal biomass‐attenuation relationships are analyzed by (1) considering the rather regular change of the living‐to‐detrital organic carbon ratio which seems to occur in oceanic waters ranging from oligotrophic to eutrophic, and (2) accounting for the respective contributions of absorption (by pigmented cells) and of scattering (by all kind of particulates) in the attenuation process of radiant energy.

The apparent optical properties (AOPs) of oceanic case 1 waters were previously analyzed [ Morel , 1988] and statistically related to the chlorophyll concentration ([Chl]) used as a global index describing the trophic conditions of water bodies. From these empirical relationships a bio‐optical model of the upper layer was developed. With objectives and structure similar to those of the previous study the present reappraisal utilizes AOPs determined during recent Joint Global Ocean Flux Study cruises, namely, spectral attenuation for downward irradiance K d (λ) and irradiance reflectance R (λ). This revision also benefits from improved knowledge of inherent optical properties (IOPs), namely, pure water absorption coefficients and particle scattering and absorption coefficients, and from better pigment quantification (via a systematic use of high‐performance liquid chromatography). Nonlinear trends, already observed between optical properties and algal biomass, are fully confirmed, yet with numerical differences. The previous K d (λ) model, and subsequently the R (λ) model, is modified to account for these new relationships. The R (λ) values predicted as a function of [Chl] and the predicted ratios of reflectances at two wavelengths, which are commonly used in ocean color algorithms, compare well with field values (not used when developing the reflectance model). This good agreement means that semianalytical ocean color algorithms can be successfully applied to satellite data. Going further into purely analytical approaches, ideally based on radiative transfer computations combined with a suite of relationships between the IOPs and [Chl], remains presently problematic, especially because of the insufficient knowledge of the phase function and backscattering efficiency of oceanic particles.

Variability in the chlorophyll (chl) a ‐specific absorption coefficients of living phytoplankton a ph * (λ) was analyzed using a data set including 815 spectra determined with the wet filter technique in different regions of the world ocean (covering the chlorophyll concentration range 0.02–25 mg m −3 ). The a ph * values were observed to decrease rather regularly from oligotrophic to eutrophic waters, spanning over more than 1 order of magnitude (0.18 to 0.01 m 2 mg −1 ) at the blue absorption maximum. The observed covariation between a ph * (λ) and the field chl a concentration (chl) can be explained considering (1) the level or pigment packaging and (2) the contribution of accessory pigments to absorption. Empirical relationships between a ph * (λ) and 〈chl〉 were derived by least squares fitting to power functions. These relationships can be used to produce a ph * spectra as a function of 〈chl〉. Such a simple parameterization, if confirmed with further data, can be used, e.g., for refining estimates of the carbon fixation rate at global or regional scales, such as those obtained by combining satellite pigment concentration maps with primary production models based on physiological parameters, among which a ph * is an important one.

A fast method has been proposed [ Antoine and Morel , this issue] to compute the oceanic primary production from the upper ocean chlorophyll‐like pigment concentration, as it can be routinely detected by a spaceborne ocean color sensor. This method is applied here to the monthly global maps of the photosynthetic pigments that were derived from the coastal zone color scanner (CZCS) data archive [ Feldman et al. , 1989]. The photosynthetically active radiation (PAR) field is computed from the astronomical constant and by using an atmospheric model, thereafter combined with averaged cloud information, derived from the International Satellite Cloud Climatology Project (ISCCP). The aim is to assess the seasonal evolution, as well as the spatial distribution of the photosynthetic carbon fixation within the world ocean and for a “climatological year”, to the extent that both the chlorophyll information and the cloud coverage statistics actually are averages obtained over several years. The computed global annual production actually ranges between 36.5 and 45.6 Gt C yr −1 according to the assumption which is made (0.8 or 1) about the ratio of active‐to‐total pigments (recall that chlorophyll and pheopigments are not radiometrically resolved by CZCS). The relative contributions to the global productivity of the various oceans and zonal belts are examined. By considering the hypotheses needed in such computations, the nature of the data used as inputs, and the results of the sensitivity studies, the global numbers have to be cautiously considered. Improving the reliability of the primary production estimates implies (1) new global data sets allowing a higher temporal resolution and a better coverage, (2) progress in the knowledge of physiological responses of phytoplankton and therefore refinements of the time and space dependent parameterizations of these responses.

The variations of the spectral absorption coefficient of seawater can be attributed to three principal factors—phytoplankton, nonchlorophyllous particles, and yellow substances— whose concentrations are represented in this study in terms of chlorophyll a and pheophytin a content ( C ), the total scattering coefficient ( b ), and the absorption by filtered seawater at a given wavelength ( Y ). By assuming an exponential absorption by yellow substances, we developed a new iterative method for identifying the in situ apparent specific spectral absorption curves of the other two factors. The weighting coefficients for each of the three components are calculated for over 80 spectral absorption measurements from different representative marine regions. The reconstruction of spectral absorption curves from the three coefficients and the three specific absorption curves fits the original data with an overall average error of 3%. Relationships between these coefficients and C , b, and Y are examined. Results show that, though the spectral form of absorption by pigments can be considered as more or less invariant, the absorption “efficiency” per unit C depends on the nature of the water, and hence on the type of phytoplankton population considered. An optical classification based on the three optical coefficients related to three absorbing agents is proposed.

Maps of surface chlorophyllous pigment (Chl a + Pheo a ) are currently produced from ocean color sensors. Transforming such maps into maps of primary production can be reliably done only by using light‐production models in conjunction with additional information about the column‐integrated pigment content and its vertical distribution. As a preliminary effort in this direction, ∼4,000 vertical profiles of pigment (Chl a + Pheo a ) determined only in oceanic Case 1 waters have been statistically analyzed. They were scaled according to dimensionless depths (actual depth divided by the depth of the euphotic layer, Z e ) and expressed as dimensionless concentrations (actual concentration divided by the mean concentration within the euphotic layer). The depth Z e , generally unknown, was computed with a previously developed bio‐optical model. Highly significant relationships were found allowing 〈 C 〉 tot the pigment content of the euphotic layer, to be inferred from the surface concentration, C ̄ pd , observed within the layer of one penetration depth. According to their C ̄ d values (ranging from 0.01 to >10 mg m −3 ), we categorized the profiles into seven trophic situations and computed a mean vertical profile for each. Between a quasi‐uniform profile in eutrophic waters and a profile with a strong deep maximum in oligotrophic waters, the shape evolves rather regularly. The well‐mixed cold waters, essentially in the Antarctic zone, have been separately examined. On average, their profiles are featureless, without deep maxima, whatever their trophic state. Averaged values of ρ , the ratio of Chl a to (Chl a + Pheo a ), have also been obtained for each trophic category. The energy stored by photosynthesizing algae, once normalized with respect to the integrated chlorophyll biomass 〈 C 〉 tot is proportional to the available photosynthetic energy at the surface via a parameter ψ *, which is the cross‐section for photosynthesis per unit of areal chlorophyll. By taking advantage of the relative stability of ψ *, we can compute primary production from ocean color data acquired from space. For such a computation, inputs are the irradiance field at the ocean surface, the “surface” pigment from which 〈 C 〉 tot can be derived, the mean ρ value pertinent to the trophic situation as depicted by the C ̄ pd or 〈C〉 tot values, and the cross‐section ψ *. Instead of a constant ψ * value, the mean profiles can be used; they allow the climatological field of the ψ * parameter to be adjusted through the parallel use of a spectral light‐production model.

Spectral absorption coefficients of total particulate matter a p (λ) were determined using the in vitro filter technique. The present analysis deals with a set of 1166 spectra, determined in various oceanic (case 1) waters, with field chl a concentrations (〈chl〉) spanning 3 orders of magnitude (0.02–25 mg m −3 ). As previously shown [ Bricaud et al. , 1995] for the absorption coefficients of living phytoplankton a ø (λ), the a p (λ) coefficients also increase nonlinearly with 〈chl〉. The relationships (power laws) that link a p (λ) and a ø (λ) to 〈chl〉 show striking similarities. Despite large fluctuations, the relative contribution of nonalgal particles to total absorption oscillates around an average value of 25–30% throughout the 〈chl〉 range. The spectral dependence of absorption by these nonalgal particles follows an exponential increase toward short wavelengths, with a weakly variable slope (0.011±0.0025 nm −1 ). The empirical relationships linking a p (λ) to (〈chl〉) can be used in bio‐optical models. This parameterization based on in vitro measurements leads to a good agreement with a former modeling of the diffuse attenuation coefficient based on in situ measurements. This agreement is worth noting as independent methods and data sets are compared. It is stressed that for a given (〈chl〉), the a p (λ) coefficients show large residual variability around the regression lines (for instance, by a factor of 3 at 440 nm). The consequences of such a variability, when predicting or interpreting the diffuse reflectance of the ocean, are examined, according to whether or not these variations in a p are associated with concomitant variations in particle scattering. In most situations the deviations in a p actually are not compensated by those in particle scattering, so that the amplitude of reflectance is affected by these variations.

Cats are generalist predators that have been widely introduced to the world's ~179 000 islands. Once introduced to islands, cats prey on a variety of native species many of which lack evolved defenses against mammalian predators and can suffer severe population declines and even extinction. As islands house a disproportionate share of terrestrial biodiversity, the impacts of invasive cats on islands may have significant biodiversity impacts. Much of this threatened biodiversity can be protected by eradicating cats from islands. Information on the relative impacts of cats on different native species in different types of island ecosystems can increase the efficiency of this conservation tool. We reviewed feral cat impacts on native island vertebrates. Impacts of feral cats on vertebrates have been reported from at least 120 different islands on at least 175 vertebrates (25 reptiles, 123 birds, and 27 mammals), many of which are listed by the International Union for the Conservation of Nature. A meta-analysis suggests that cat impacts were greatest on endemic species, particularly mammals and greater when non-native prey species were also introduced. Feral cats on islands are responsible for at least 14% global bird, mammal, and reptile extinctions and are the principal threat to almost 8% of critically endangered birds, mammals, and reptiles.

On the basis of phenotypical characteristics and analysis of 16S rRNA sequence, a new species belonging to a new genus is described, and the name Marinobacter hydrocarbonoclasticus is proposed. This organism, isolated from Mediterranean seawater near a petroleum refinery, is a gram-negative, aerobic, rod-shaped bacterium. It grows at NaCl concentrations of 0.08 to 3.5 M and uses various hydrocarbons as the sole source of carbon and energy. Its DNA has a guanine-plus-cytosine content of 52.7 mol%. The 16S rRNA analysis shows a clear affiliation between M. hydrocarbonoclasticus and the gamma group of the phylum Proteobacteria. A close phylogenetic relationship appears among the species Marinomonas vaga, Oceanospirillum linum, Halomonas elongata, and Pseudomonas aeruginosa. Because of the impossibility of finding a single most closely related species, we suggest that this bacterium be assigned to a new genus, at least temporarily. The possibility of a revision of this status when new data appear is, however, not excluded. The type strain is M. hydrocarbonoclasticus SP.17 (= ATCC 49840).

Seven models for computing underwater radiances and irradiances by numerical solution of the radiative transfer equation are compared. The models are applied to the solution of several problems drawn from optical oceanography. The problems include highly absorbing and highly scattering waters, scattering by molecules and by particulates, stratified water, atmospheric effects, surface-wave effects, bottom effects, and Raman scattering. The models provide consistent output, with errors (resulting from Monte Carlo statistical fluctuations) in computed irradiances that are seldom larger, and are usually smaller, than the experimental errors made in measuring irradiances when using current oceanographic instrumentation. Computed radiances display somewhat larger errors.

Absorption coefficients of total particulate (biogenous) matter were determined in the mesotrophic waters of the Peruvian upwelling and the oligotrophic waters of the Sargasso Sea. A method based on spectral criteria was used to partition these coefficients into absorption by living algal cells and by nonalgal (mainly detrital) material. This method was tested by independently measuring absorption by nonalgal material for samples from the Sargasso Sea. The average Chl‐specific absorption coefficients measured in the Sargasso Sea are significantly higher than in the Peruvian upwelling and also higher in the surface layer than in the deep Chl maximum layer. These systematic variations appear to be mainly due to differences in sizes and intracellular pigment concentrations of the cells, inducing differences in the amplitude of the package effect.

Serpentinites are an important component of the oceanic crust generated in slow to ultraslow spreading settings. In this context, the MOHO likely corresponds to a hydration boundary, which could match the 500 °C isotherm beneath the ridge axis. Textures from serpentinites sampled in ridge environments demonstrate that most of the serpentinization occurs under static conditions. The typical mineralogical association consists of lizardite ± chrysotile + magnetite ± tremolite ± talc. Despite the widespread occurrence of lizardite, considered as the low temperature serpentine variety, oxygen isotope fractionation suggests that serpentinization starts at high temperature, in the range of 300–500 °C. The fluid responsible for serpentinization is seawater, possibly evolved by interaction with the crust. Compared with fresh peridotites, serpentinites are strongly hydrated (10–15% H 2 O) and oxidized. Serpentinization, however, does not seem to be accompanied by massive leaching of major elements, implying that it requires a volume increase. It results in an increase in chlorine, boron, fluorine, and sulfur, but its effect on other trace elements remains poorly detailed. The presence of serpentinites in the oceanic crust affects its physical properties, in particular by lowering its density and seismic velocities, and modifying its magnetic and rheological properties. Serpentinization may activate hydrothermal cells and generate methane and hydrogen anomalies which can sustain microbial communities. Two types of hydrothermal field have been identified: the Rainbow type, with high temperature (360 °C) black smokers requiring magmatic heat; the low temperature (40–75 °C) Lost City type, by contrast, can be activated by serpenintization reactions.

We used simplifying assumptions to derive analytical formulae expressing the reflectance of shallow waters as a function of observation depth and of bottom depth and albedo. These formulae also involve two apparent optical properties of the water body: a mean diffuse attenuation coefficient and a hypothetical reflectance which would be observed if the bottom was infinitely deep. The validity of these approximate formulae was tested by comparing their outputs with accurate solutions of the radiative transfer obtained under the same boundary conditions by Monte Carlo simulations. These approximations were also checked by comparing the reflectance spectra for varying bottom depths and compositions determined in coastal lagoons with those predicted by the formulae. These predictions were based on separate determinations of the spectral albedos of typical materials covering the floor, such as coral sand and various green or brown algae. The simple analytical expressions are accurate enough for most practical applications and also allow quantitative discussion of the limitations of remote‐sensing techniques for bottom recognition and bathymetry.

For visible wavelengths and for most of the oceanic waters, the albedo for single scattering (?) is not high enough to generate within the upper layers of the ocean a completely diffuse regime, so that the upwelling radiances below the surface, as well as the water-leaving radiances, generally do not form an isotropic radiant field. The nonisotropic character and the resulting bidirectional reflectance are conveniently expressed by the Q factor, which relates a given upwelling radiance L(u) (θ',φ) to the upwelling irradiance E(u) (θ' is the nadir angle, φ is the azimuth angle, and Q = E(u)/L(u)); in addition the Q function is also dependent on the Sun's position. Another factor, denoted f, controls the magnitude of the global reflectance, R (= E(u) /E(d), where E(d) is the downwelling irradiance below the surface); f relates R to the backscattering and absorption coefficients of the water body (b(b) and a, respectively), according to R = f(b(b)/a). This f factor is also Sun angle dependent. By operating an azimuth-dependent Monte Carlo code, both these quantities, as well as their ratio (f/Q) have been studied as a function of the water optical characteristics, namely ? and η; η is the ratio of the molecular scattering to the total (molecular + particles) scattering. Realistic cases (including oceanic waters, with varying chlorophyll concentrations; several wavelengths involved in the remote sensing of ocean color and variable atmospheric turbidity) have been considered. Emphasis has been put on the geometrical conditions that would be typical of a satellite-based ocean color sensor, to derive and interpret the possible variations of the signal emerging from various oceanic waters, when seen from space under various angles and solar illumination conditions.

Salt-tolerant plants grow in a wide variety of saline habitats, from coastal regions, salt marshes and mudflats to inland deserts, salt flats and steppes. Halophytes living in these extreme environments have to deal with frequent changes in salinity level. This can be done by developing adaptive responses including the synthesis of several bioactive molecules. Consequently, several salt marsh plants have traditionally been used for medical, nutritional, and even artisanal purposes. Currently, an increasing interest is granted to these species because of their high content in bioactive compounds (primary and secondary metabolites) such as polyunsaturated fatty acids, carotenoids, vitamins, sterols, essential oils (terpenes), polysaccharides, glycosides, and phenolic compounds. These bioactive substances display potent antioxidant, antimicrobial, anti-inflammatory, and anti-tumoral activities, and therefore represent key-compounds in preventing various diseases (e.g. cancer, chronic inflammation, atherosclerosis and cardiovascular disorder) and ageing processes. The ongoing research will lead to the utilisation of halophytes as a new source of healthy products as functional foods, nutraceuticals or active principles in several industries. This contribution focuses on the ethnopharmacological uses of halophytes in traditional medicine and reviews recent investigations on their biological activities and nutraceuticals. The work is distributed according to the different families of nutraceuticals (lipids, vitamins, proteins, glycosides, phenolic compounds, etc.) discussing the analytical techniques employed for their determination. Information about the claimed health promoting effects of the different families of nutraceuticals is also provided together with data on their application.

Pseudomonas aeruginosa is a Gram-negative bacterium belonging to the γ-proteobacteria. Like other members of the Pseudomonas genus, it is known for its metabolic versatility and its ability to colonize a wide range of ecological niches, such as rhizosphere, water environments and animal hosts, including humans where it can cause severe infections. Another particularity of P. aeruginosa is its high intrinsic resistance to antiseptics and antibiotics, which is partly due to its low outer membrane permeability. In contrast to Enterobacteria, pseudomonads do not possess general diffusion porins in their outer membrane, but rather express specific channel proteins for the uptake of different nutrients. The major outer membrane 'porin', OprF, has been extensively investigated, and displays structural, adhesion and signaling functions while its role in the diffusion of nutrients is still under discussion. Other porins include OprB and OprB2 for the diffusion of glucose, the two small outer membrane proteins OprG and OprH, and the two porins involved in phosphate/pyrophosphate uptake, OprP and OprO. The remaining nineteen porins belong to the so-called OprD (Occ) family, which is further split into two subfamilies termed OccD (8 members) and OccK (11 members). In the past years, a large amount of information concerning the structure, function and regulation of these porins has been published, justifying why an updated review is timely.

The upwelling radiance field beneath the ocean surface and the emerging radiance field are not generally isotropic. Their bidirectional structure depends on the illumination conditions (the Sun's position in particular) and on the optical properties of the water body. In oceanic case 1 waters, these properties can be related, for each wavelength λ, to the chlorophyll (Chl) concentration. We aim to quantify systematically the variations of spectral radiances that emerge from an ocean with varying Chl when we change the geometric conditions, namely, the zenith-Sun angle, the viewing angle, and the azimuth difference between the solar and observational vertical planes. The consequences of these important variations on the interpretation of marine signals, as detected by a satelliteborne ocean color sensor, are analyzed. In particular, the derivation of radiometric quantities, such as R (λ), the spectral reflectance, or [ L(w)(λ)](N), the normalized water-leaving radiance that is free from directional effects, is examined, as well as the retrieval of Chl. We propose a practical method that is based on the use of precomputed lookup tables to provide values of the f/Q ratio in all the necessary conditions[ f relates (R(λ) to the backscattering and absorption coefficients, whereas Q is the ratio of upwelling irradiance to any upwelling radiance]. The f/Q ratio, besides being dependent on the geometric configuration (the three angles mentioned above), also varies with λ and with the bio-optical state, conveniently depicted by Chl. Because Chl is one of the entries for the lookup table, it has to be derived at the beginning of the process, before the radiometric quantities R(λ) or [L(W)(λ)](N) can be produced. The determination of Chl can be made through an iterative process, computationally fast, using the information at two wavelengths. In this attempt to remove the bidirectional effect, the commonly accepted view relative to the data-processing strategy is somewhat modified, i.e., reversed, as the Chl index becomes a prerequisite parameter that must be identified prior to the derivation of the fundamental radiometric quantities at all wavelengths.

We describe an approach to modeling the ocean's inherent optical properties (IOPs) that permits extensive analyses of IOPs as the detailed composition of suspended particulate matter is varied in a controlled manner. Example simulations of the IOP model, which includes 18 planktonic components covering a size range from submicrometer viruses and heterotrophic bacteria to microplanktonic species of 30-mum cell diameter, are discussed. Input data to the model include the spectral optical cross sections on a per particle basis and the particle-number concentration for each individual component. This approach represents a significant departure from traditional IOP and bio-optical models in which the composition of seawater is described in terms of a few components only or chlorophyll concentration alone. The simulations illustrate how the separation and understanding of the effects of various types of particle present within a water body can be achieved. In an example simulation representing an oligotrophic water body with a chlorophyll a concentration of 0.18 mg m(-3), the planktonic microorganisms altogether are the dominant particulate component in the process of light absorption, but their relative contribution to light scattering is smaller than that of nonliving particles. A series of simulations of water bodies with the same chlorophyll a concentration but dominated by different phytoplankton species shows that composition of the planktonic community is an important source of optical variability in the ocean.

A global assessment of carbon flux in the world ocean is one of the major undertakings of the Joint Global Ocean Flux Study (JGOFS). This has to be undertaken using historical in situ data of primary productivity. As required by the temporal and spatial scales involved in a global study, it can be conveniently done by combining, through appropriate models, remotely sensed information (chlorophyll a, temperature) with basic information about the parameters related to the carbon uptake by phytoplanktonic algae. This requires a better understanding as well as a more extended knowledge of these parameters which govern the radiative energy absorption and utilization by algae in photosynthesis. The measurement of the photosynthetic response of algae [ photosynthesis (P) versus it-radiance (E) curves], besides being less shiptime consuming than in situ primary production experiments, allows the needed parameters to be derived and systematically studied as a function of the physical, chemical and ecological conditions. The aim of the present paper is to review the sig nificance of these parameters, especially in view of their introduction into models, to analyze the causes of their variations in the light of physiological considerations, and finally to provide methodo logical recommendations for meaningful determinations, and interpretation, of the data resulting from P versus E determinations. Of main concern are the available and usable irradiance, the chloro phyll a-specific absorption capabilities of the algae, the maximum light utilization coefficient (cs), the maximum quantum yield (φm)( the maximum photosynthetic rate (Pm) and the light saturation index (EL). The potential of other, non-intrusive, approaches, such as the stimulated variable fluorescence, or the sun-induced natural fluorescence techniques is also examined.

UV radiation (UVR) is a significant ecological factor in the marine environment that can have important effects on planktonic organisms and dissolved organic matter (DOM). The penetration of UVR into the water column is likely to change in the near future due to interactions between global warming and ozone depletion. In this study we report underwater instruments employed for the measurement of UVR and we review data dealing with the depth of UVR penetration in different oceanic areas including the open ocean, Antarctic waters and coastal waters. We provide the 10% irradiance depth (Z10%) for UV-A and UV-B as well as for DNA damage effective dose (DNA), which we calculated from the values of diffuse attenuation coefficients or vertical profiles reported in the literature. We observe a clear distinction between open ocean (high Z10%, no variation in the ratio UV-B/UV-A), Antarctic waters (increase in the ratio UV-B/UV-A during ozone hole conditions) and coastal waters (low Z10%, no variation in the ratio UV-B/UV-A). These variations in the penetration of UVR could lead to differences in the relative importance of photobiological/photochemical processes. We also compare in this study the penetration of UV-B (unweighted and weighted by the Setlow action spectrum) and DNA damage effective dose.