Timothy J. Smyth

The seasonal structure of microbial communities in the Western English Channel

Very few marine microbial communities are well characterized even with the weight of research effort presently devoted to it. Only a small proportion of this effort has been aimed at investigating temporal community structure. Here we present the first report of the application of high-throughput pyrosequencing to investigate intra-annual bacterial community structure. Microbial diversity was determined for 12 time points at the surface of the L4 sampling site in the Western English Channel. This was performed over 11 months during 2007. A total of 182 560 sequences from the V6 hyper-variable region of the small-subunit ribosomal RNA gene (16S rRNA) were obtained; there were between 11 327 and 17 339 reads per sample. Approximately 7000 genera were identified, with one in every 25 reads being attributed to a new genus; yet this level of sampling far from exhausted the total diversity present at any one time point. The total data set contained 17 673 unique sequences. Only 93 (0.5%) were found at all time points, yet these few lineages comprised 50% of the total reads sequenced. The most abundant phylum was Proteobacteria (50% of all sequenced reads), while the SAR11 clade comprised 21% of the ubiquitous reads and approximately 12% of the total sequenced reads. In contrast, 78% of all operational taxonomic units were only found at one time point and 67% were only found once, evidence of a large and transient rare assemblage. This time series shows evidence of seasonally structured community diversity. There is also evidence for seasonal succession, primarily reflecting changes among dominant taxa. These changes in structure were significantly correlated to a combination of temperature, phosphate and silicate concentrations.

Radiative forcing of climate by hydrochlorofluorocarbons and hydrofluorocarbons

We measure infrared absorption spectra of 18 hydrochlorofluorocarbons and hydrofluorocarbons, seven of which do not yet appear in the literature. The spectra are used in a narrowband model of the terrestrial infrared radiation to calculate radiative forcing and global warming potentials. We investigate the sensitivity of the radiative forcing to the absorption spectrum temperature dependence, halocarbon vertical profile, stratospheric adjustment, cloudiness, spectral overlap, and latitude, and we make some recommendations for the reporting of radiative forcings that would help to resolve discrepancies between assessments. We investigate simple methods of estimating instantaneous radiative forcing directly from a molecules absorption spectrum and we present a new method that agrees to within 0.3% with our narrowband model results.

Maritime Aerosol Network as a component of Aerosol Robotic Network

The paper presents the current status of the Maritime Aerosol Network (MAN), which has been developed as a component of the Aerosol Robotic Network (AERONET). MAN deploys Microtops handheld Sun photometers and utilizes the calibration procedure and data processing (Version 2) traceable to AERONET. A web site dedicated to the MAN activity is described. A brief historical perspective is given to aerosol optical depth (AOD) measurements over the oceans. A short summary of the existing data, collected on board ships of opportunity during the NASA Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) Project is presented. Globally averaged oceanic aerosol optical depth (derived from island-based AERONET measurements) at 500 nm is similar to 0.11 and Angstrom parameter (computed within spectral range 440-870 nm) is calculated to be similar to 0.6. First results from the cruises contributing to the Maritime Aerosol Network are shown. MAN ship-based aerosol optical depth compares well to simultaneous island and near-coastal AERONET site AOD.

Generalized ocean color inversion model for retrieving marine inherent optical properties

Ocean color measured from satellites provides daily, global estimates of marine inherent optical properties (IOPs). Semi-analytical algorithms (SAAs) provide one mechanism for inverting the color of the water observed by the satellite into IOPs. While numerous SAAs exist, most are similarly constructed and few are appropriately parameterized for all water masses for all seasons. To initiate community-wide discussion of these limitations, NASA organized two workshops that deconstructed SAAs to identify similarities and uniqueness and to progress toward consensus on a unified SAA. This effort resulted in the development of the generalized IOP (GIOP) model software that allows for the construction of different SAAs at runtime by selection from an assortment of model parameterizations. As such, GIOP permits isolation and evaluation of specific modeling assumptions, construction of SAAs, development of regionally tuned SAAs, and execution of ensemble inversion modeling. Working groups associated with the workshops proposed a preliminary default configuration for GIOP (GIOP-DC), with alternative model parameterizations and features defined for subsequent evaluation. In this paper, we: (1) describe the theoretical basis of GIOP; (2) present GIOP-DC and verify its comparable performance to other popular SAAs using both in situ and synthetic data sets; and, (3) quantify the sensitivities of their output to their parameterization. We use the latter to develop a hierarchical sensitivity of SAAs to various model parameterizations, to identify components of SAAs that merit focus in future research, and to provide material for discussion on algorithm uncertainties and future emsemble applications.

Semianalytical model for the derivation of ocean color inherent optical properties: description, implementation, and performance assessment

A semianalytical approach to the problem of determining inherent optical properties from satellite and in situ ocean color data is presented. The model uses empirically derived spectral slopes between neighboring wavebands in combination with radiative transfer modeling to determine the spectral absorption (alpha) and backscatter (b(b)); these values are then further decomposed into absorption due to phytoplankton, detrital, and colored dissolved organic matter components. When compared with over 400 in situ data points the model makes good retrievals of the total absorption and backscatter across the entire spectrum, with regression slopes close to unity, little or no bias, high percentage of variance explained, and low rms errors.

Retrieval of coccolithophore calcite concentration from SeaWiFS Imagery

We examined blooms of the coccolithophorid E. huxleyi, observed in SeaWiFS imagery, with a new algorithm for the retrieval of detached coccolith concentration. The algorithm uses only SeaWiFS bands in the red and near infrared (NIR) to minimize the influence of the absorption by chlorophyll and dissolved organic material. We used published experimental determinations of the calcite specific backscattering and its spectral dependence, and assumed that the absorption coefficient of the medium was that of pure water, to estimate the marine contribution to the SeaWiFS radiance. The aerosol (and Rayleigh-aerosol interaction) contribution to the radiance was modeled as an exponential function of wavelength. These allow derivation of the coccolith concentration on a pixel-by-pixel basis from SeaWiFS imagery. Application to a July 30, 1999 SeaWiFS image of a bloom south of Plymouth, UK indicates that the SeaWiFS estimates are in good agreement with surface measurements of coccolith concentration.

Modelling the global coastal ocean

Shelf and coastal seas are regions of exceptionally high biological productivity, high rates of biogeochemical cycling and immense socio-economic importance. They are, however, poorly represented by the present generation of Earth system models, both in terms of resolution and process representation. Hence, these models cannot be used to elucidate the role of the coastal ocean in global biogeochemical cycles and the effects global change (both direct anthropogenic and climatic) are having on them. Here, we present a system for simulating all the coastal regions around the world (the Global Coastal Ocean Modelling System) in a systematic and practical fashion. It is based on automatically generating multiple nested model domains, using the Proudman Oceanographic Laboratory Coastal Ocean Modelling System coupled to the European Regional Seas Ecosystem Model. Preliminary results from the system are presented. These demonstrate the viability of the concept, and we discuss the prospects for using the system to explore key areas of global change in shelf seas, such as their role in the carbon cycle and climate change effects on fisheries.

Remote sensing of sea surface temperature and chlorophyll during Lagrangian experiments at the Iberian margin

Satellite derived sea surface temperature (SST) and chlorophyll data are used to characterise the period of upwelling during a cruise on which two Lagrangian drift experiments were conducted off the Iberian Atlantic coast in August 1998. During the cruise there was a prolonged period of equator-ward winds which favour upwelling; three distinct maxima were observed in the meteorological data interspersed with periods of relaxation. The SST and chlorophyll imagery show upwelling to be active with distinct offshore filaments that are cooler and of higher chlorophyll concentration than the surrounding oceanic water; these filaments represent an important cross-shelf transport mechanism. A front detection methodology has been applied to satellite images and suggests that these filaments are distinct, long-lived features, characterised by enhanced primary production.

Spawning season and temperature relationships for sardine (Sardina pilchardus) in the eastern North Atlantic

Spawning temperature preferences for sardine (Sardina pilchardus) in the eastern North Atlantic were determined from egg survey data. These were compared with climatological temperature cycles (1986 2002) derived from satellite observations, by geographical region, to predict spawning seasons. Optimum spawning temperatures were determined as 14.0-15.0°C from the English Channel to Portugal and 16.0-18.0°C for all north-west African regions. Spawning seasons were closely related to the general latitudinal trend of the annual temperature cycle, with modification by upwelling in the western Iberian and north-west African regions. Some differences between temperature-based spawning season predictions and field observations were related to variations in seasonal plankton production. Correlations in the annual time-series of favourable spawning temperatures suggested relatively strong linkages between the southern areas from Portugal to Senegal. There was no consistent relationship between annual variations in extent of temperature-predicted spawning seasons and observed field abundance of eggs.

The response of phytoplankton production to periodic upwelling and relaxation events at the Iberian shelf break: estimates by the 14C method and by satellite remote sensing

Abstract The primary productivity of the NW Iberian margin has been determined by a combination of 14 C incorporation experiments on natural phytoplankton assemblages and satellite remote sensing with the ocean colour sensor, SeaWiFS. The approach to the field determination of phytoplankton production was Eulerian, involving measurements on a fixed grid of stations covering the region from 41°30′N to 43°00′N and 09°00′W to 10°30′W. Three different laboratories made primary production measurements over a 3-year period. Each group used variations of the 14 C method—in situ incubations and two modelling approaches based on P – E parameter derivation. An intercalibration experiment showed acceptable agreement between the three estimates. Measurements by the three groups on eight cruises have been merged to provide estimates of regional productivity. However, the temporal coverage of the data was too limited to provide robust seasonal estimates since few experiments were done in the autumn and winter months. A second approach to the estimation of primary production utilised surface pigment concentrations derived from satellite remote sensing. Two models were used. Firstly, an empirical relationship was found between depth-integrated primary production and surface chlorophyll concentration, which explained 78% of the variance in the production estimates. The second approach used a semi-analytical model which incorporates irradiance and temperature as well as chlorophyll-derived parameters. Both models have been applied to SeaWiFS-derived, surface chlorophyll concentrations to estimate primary production during 1998, 1999 and 2000 for three regions—the shelf, the slope and the open ocean of the region of study. Using the semi-analytical model, the mean primary production for the 3 years is estimated to be 319 g C m −2 year −1 for the shelf, 280 g C m −2 year −1 for the slope and 217 g C m −2 year −1 for the adjacent open ocean. Interannual variation in production on the shelf ranged from 334 g C m −2 year −1 in 1998 to 301 g C m −2 year −1 in 2000. It is estimated that upwelling increased primary production, relative to that in the open ocean, by ∼50%. Satellite-derived estimates of the ratio of new production to primary production were 0.37, 0.28 and 0.40 for the shelf region during the upwelling seasons of 1998, 1999 and 2000.