Marine bio-optical properties applied to biogeochemical modelling

The seminal idea of optical oceanography is that by inspecting the colour of the ocean we can get a grasp on the biogeochemical composition of the water body. The field is used in many applications, ranging from ecology and biogeochemistry, to understanding the possible hazards in our oceans and the emerging trends of climate change. The term \u2018ocean colour\u2019 stems from the fact that the visible part of the spectrum is used by the ocean ecosystem for photosynthesis, which accounts for almost half of the global photosynthesis on Earth. The final goal of the thesis project is to improve the quality of Copernicus Marine Environment Monitoring Service (CMEMS) biogeochemical products for the Mediterranean Sea through the development of a new optical module for the MedBFM forecasting model system. CMEMS products quality assessment requires the comparison of model outputs with observations and the use of specific metrics. A quality-controlled bio-optical in-situ data set from the Biogeochemical-Argo Mediterranean floats network (BGC-Argo, with 4 radiometric, 2 physical and 1 biogeochemical variable) and remote sensing products from the Copernicus Marine Data Stream (inter-annually variable weekly data of diffuse attenuation coefficients of downward planar irradiance, Kd(var), at 490 nm) were used for such purpose. In both cases, the optical data (PAR profiles and Kd(490) maps respectively) served as model input for the MedBFM system (in 1- and 3-dimensional settings), whilst the biogeochemical data from BGC-Argo floats (fluorescence derived chlorophyll concentration profiles) and HPLC-obtained chlorophyll data from an openly accessible database were used for validation purposes. The work included two different MedBFM model configurations: firstly, in the form of a non-assimilative 1-dimensional model with various bio-optical and mixing parametrizations, where the former might serve both as a first step towards more complex optical representations and could on the other hand have a diagnostic utility by inspecting the product quality through the use of BGC-Argo floats. The combined use of a biogeochemical model of medium complexity) with a rich data set enabled also an in-depth study on the optics-related biogeochemical properties of the examined basin. The second configuration focused on the impact of using weekly variable Kd(var) versus climatological Kd(clim) values as a full 3-dimensional model optical forcing, thus estimating the effect of an updated data set in terms of spatio-temporal variability of the chlorophyll field and output quality. Such an integrated approach is useful as a first step towards the improvement of the new optical component of the 3-dimensional biogeochemical Mediterranean Sea model, striving towards the implementation of a hyperspectral radiative transfer model, which would present a fundamental upgrade to obtain a more accurate description of the underwater light field, impacting both biogeochemistry and hydrodynamics

A high-resolution hydrodynamic-biogeochemical coupled model of the Gulf of Cadiz – Alboran Sea region.

The southern Iberia regional seas comprise the Gulf of Cadiz and the Alboran Sea sub-basins connected by the narrow Strait of Gibraltar. Both basins are very different in their hydrological and biological characteristics but are, also, tightly connected to each other. Integrative studies of the whole regional oceanic system are scarce and difficult to perform due to the relative large area to cover and the different relevant time-scales of the main forcings in each sub-basin. Here we propose, for the first time, a fully coupled, 3D, hydrodynamic-biogeochemical model that covers, in a single domain (~2km resolution) both marine basins for a 20 years simulation (1989-2008). Model performance is assessed against available data in terms of spatial and temporal distributions of biological variables. In general, the proposed model is able to represent the climatological distributions of primary and secondary producers and also the main seasonality of primary production in the different sub-regions of the analyzed basins. Potential causes of the observed mismatches between model and data are identified and some solutions are proposed for future model development. We conclude that most of these mismatches could be attributed to the missing tidal forcing in the actual model configuration. This model is a first step to obtain a meaningful tool to study past and future oceanographic conditions in this important marine region constituting the unique connection of the Mediterranean Sea with the open world’s ocean

Surface mesoscale pico–nanoplankton patterns at the main fronts of the Alboran Sea

© 2014 Elsevier B.V. The mesoscale (10-100. km, days-weeks) plays a key role in the Ocean's ecosystem structure and dynamics. This work compares the pico-nanoplankton patterns observed in the Alboran Sea (Western Mediterranean) during three oceanographic cruises. We analyse its response to different expressions of mesoscale circulation associated with the three major hydrodynamic features in the basin; namely the Northwestern Alboran Front (NWAF, surveyed in OMEGA-1 cruise), the Almeria-Oran Front (AOF, surveyed in OMEGA-2 cruise) and the Western Alboran Gyre (WAG, surveyed in BIOMEGA cruise). The first two surveys were carried out under the most typical quasi-stationary twin gyre conditions of the Alboran Sea, whereas the third cruise was performed after an eastward migration of the WAG. The analysis of pico and nanoplankton populations was carried out using flow cytometry. The patchiness observed in the three cruises indicates an association of phytoplankton peaks with the main frontal structures: abundances were higher in the NWAF/upwelling area in OMEGA-1, at the Mediterranean side of the AOF in OMEGA-2, and at a tongue of recent Atlantic Water west of the WAG in BIOMEGA. However, a more detailed analysis reveals that different factors explain the origin of the phytoplankton biomass in each front/cruise. Mixing processes at the Strait of Gibraltar and the subsequent advection of water properties into the Western Alboran Sea were the mechanisms responsible for the abundances observed in the NWAF. The highest concentrations observed in the AOF were related to the intrusion of Mediterranean Surface Waters to the north of the front. During the migrating WAG the phytoplankton distribution was influenced by the formation of a new gyre. The relation between phytoplankton and mesoscale dynamics is further explored in terms of vertical velocity diagnosis. In all cases, intense vertical motion is negatively correlated with the abundance of phytoplankton populations. This resulted from the intense geostrophic background flow associated with large vertical velocities, which drove low residence times of water mass properties and hence a weak biological response. Fast-repeated surveys made during the OMEGA-1 and OMEGA-2 cruises reveal that the surveyed hydrographic features are subjected to significant temporal variability. In this case, the impact on the biology is most evident at taxa level.This work was partially supported by the EU funded MAST project OMEGA (MAS3-CT95-0001) and by the BIOMEGA project, funded by the Spanish Marine Science and Technology Program (REN2002-04044-C02-02). P. Leon was financed by a FPI grant from the Spanish Ministry of Education and Science (BES-2003-1032)Peer Reviewe

Bio-Optical Environmental Assessments of Marginal Seas - Progress Report2

Algal blooms in the Mediterranean Sea have been studied by means of SeaWiFS derived (1998-2003) data on chlorophyll-like pigment concentration. Statistics of blooming anomalies, as well as comparisons with analogous data collected in situ, were used to address the relationship between local and regional phytoplankton dynamics, in both the (mesotrophic, sometimes eutrophic) western basin and the (oligotrophic) eastern basin. Intense (coastal) blooming appeared to be linked to local factors, and only occasionally affected by mesoscale features such as eddies or meanders, suggesting that the forcing functions of local (harmful) algal blooms and regional blooms are different, or overlap only marginally.JRC.H.5-Rural, water and ecosystem resource

In-situ, High-Frequency Assessment of Phytoplankton Functional Groups and Their Ecology in Diverse Marine Areas

Challenges ahead in phytoplankton ecology lie increasingly within the small scales, spatially and temporally, and how the diverse components of the community adapt to biotic and abiotic constraints. Despite advances made possible with new instrumentation, still little is known about the distribution of phytoplankton assemblages at the meso/submesoscale and at the diel scale. The work presented here aims at investigating phytoplankton functional groups at those scales, with a focus on their distribution and traits through time and space in different areas, and on the role of environmental factors in shaping these distribution patterns. For this purpose, a pulse-shape flow cytometer was used in-situ at high-frequency, either on-board vessels or at fixed sites, to sample ocean-to-coast gradients, and coastal areas. Besides estimating concentrations of the different functional groups, a relationship derived from cell scatter helped estimating the biomass represented by each of them, and their average cellular biomass. The total biomass of phytoplankton and the individual biomass of optically-defined groups varied significantly in relation to water masses and their properties. A refined trait-based approach was applied to qualify phytoplankton functional groups from optical features, and the diel variability of these optical features was explored. Traits were significantly correlated with several abiotic factors, mainly temperature and salinity. Multivariate ordination techniques were applied to cope with the amount of data handled and revealed patterns in phytoplankton distribution, significantly tied to hydrological features down to the submesoscale. A Cytometric Diversity Index was calculated per sample and appeared tied to water mass properties, which determined the abundance of each phytoplankton size-classes. Picophytoplankton was found to be most abundant in every location (Eastern North Atlantic, Western Mediterranean Sea, North Adriatic) and drove total phytoplankton abundance (e.g. accounting for 94.2 ± 4% in the Atlantic), while total biomass was driven by nanoeukaryotes (87 ± 6%) and occasionally by microeukaryotes (0% to 58%) and was tied both to environmental conditions and hydrological features

Análisis de los patrones de distribución de plancton en el Estrecho de Gibraltar asociados al forzamiento mareal y meteorológico

El Estrecho de Gibraltar es la única conexión entre la circulación global y el Mar Mediterráneo, el mayor cuerpo de agua semicerrado del planeta. Por lo tanto los procesos que aquí ocurren son claves para describir los flujos biogeoquímicos en la cuenca mediterránea y fundamentales para la circulación termohalina global. En el Estrecho se ha descrito una circulación “estuarina-inversa” con aguas atlánticas entrando en superficie y aguas mediterráneas más densas en profundidad. Sobre este patrón general existen alteraciones debidas al forzamiento mareal y el atmosférico o subinercial. La gran cantidad de procesos físicos y en varias escalas que ocurren en el Estrecho lo hacen muy atractivo desde el punto de vista del acoplamiento físicabiología en el ecosistema pelágico. El propósito de esta Tesis es la descripción de los patrones biogeoquímicos en el área de influencia del Estrecho, intentando cubrir un rango amplio de fenómenos con diferentes escalas espacio-temporales. Las zonas de plataforma a ambos márgenes del canal principal del Estrecho (especialmente la noroccidental) presentan una alta actividad del fitoplancton con células grandes y activas. En contraposición, la zona del canal originalmente presenta aguas oligotróficas provenientes del Golfo de Cádiz. Estas aguas oligotróficas (a través del NACW) aportan el 70% del nitrato transportado anualmente a las cuencas mediterráneas y el 55% de la biomasa fitoplanctonica. Sin embargo, existen intrusiones de aguas costeras hacia el canal relacionados con la generación de ondas internas y divergencias superficiales que éstas crean. Estos procesos se dan tanto en mareas vivas como en muertas, estando durante las vivas acompañados de alta mezcla interfacial. Los procesos derivados de las ondas internas (Tipo I) pueden significar un 30% del nitrato transportado hacia las cuencas mediterráneas, acompañadas de células activas y grandes. Este aporte también supone el 30% de la biomasa total del fitoplancton transportada. A su vez, la mezcla interfacial y adelgazamiento de la capa atlántica pueden alterar el ciclo estacional del fitoplancton de las aguas atlánticas entrantes. Estos procesos pueden aumentar la producción primaria y la biomasa, especialmente durante primavera y otoño. Estos procesos también favorecen la dominancia de nanoflagelados (primavera y otoño) y picofitoplancton (verano). Por otro lado, la turbulencia es capaz de redistribuir la biomasa del fitoplancton en vertical, siempre que existan las condiciones físico-biológicas para que se genere un máximo profundo. La relación entre turbulencia y velocidad de sedimentación del fitoplancton hace que estos máximos se sitúen bajo zonas de mayores niveles de turbulencia (mayores velocidades de sedimentación). En el futuro con mayor estratificación y mayor entrada superficial de turbulencia, la biomasa integrada de fitoplancton será menor en la capa de mezcla pero la exportación vertical de materia al océano profundo será mayor. Finalmente, los procesos ocurrentes en el Estrecho permiten que el Mar de Alborán reciba una aportación cuasi-constante de biomasa de fitoplancton y nutrientes, este último en un orden de magnitud mayor a la aportación de los afloramientos costeros descritos en esta cuenca. Estos fenómenos podrían fertilizar y mantener alta la producción primaria en esta área descrita como más productiva del Mediterráneo

The Copernicus Marine Environment Monitoring Service Ocean State Report

The Copernicus Marine Environment Monitoring Service (CMEMS) Ocean State Report (OSR) provides an annual report of the state of the global ocean and European regional seas for policy and decision-makers with the additional aim of increasing general public awareness about the status of, and changes in, the marine environment. The CMEMS OSR draws on expert analysis and provides a 3-D view (through reanalysis systems), a view from above (through remote-sensing data) and a direct view of the interior (through in situ measurements) of the global ocean and the European regional seas. The report is based on the unique CMEMS monitoring capabilities of the blue (hydrography, currents), white (sea ice) and green (e.g. Chlorophyll) marine environment. This first issue of the CMEMS OSR provides guidance on Essential Variables, large-scale changes and specific events related to the physical ocean state over the period 1993–2015. Principal findings of this first CMEMS OSR show a significant increase in global and regional sea levels, thermosteric expansion, ocean heat content, sea surface temperature and Antarctic sea ice extent and conversely a decrease in Arctic sea ice extent during the 1993–2015 period. During the year 2015 exceptionally strong large-scale changes were monitored such as, for example, a strong El Niño Southern Oscillation, a high frequency of extreme storms and sea level events in specific regions in addition to areas of high sea level and harmful algae blooms. At the same time, some areas in the Arctic Ocean experienced exceptionally low sea ice extent and temperatures below average were observed in the North Atlantic Ocean

SeaWiFS technical report series. Volume 21: The heritage of SeaWiFS. A retrospective on the CZCS NIMBUS Experiment Team (NET) program

The Sea-viewing Wide Field-of-view Sensor (SeaWiFS) mission is based on the scientific heritage of the Coastal Zone Color Scanner (CZCS), a proof-of-concept instrument carried on the National Aeronautics and Space Administration (NASA) NIMBUS-7 environmental satellite for the purpose of measuring upwelling radiance from the ocean surface. The CZCS mission provided the first observations of ocean color from space, and over the mission lifetime of 1978-1986, allowed oceanographers an initial opportunity to observe the variable patterns of global biological productivity. One of the key elements of the CZCS mission was the formation of the CZCS NIMBUS Experiment Team (NET), a group of optical physicists and biological oceanographers. The CZCS NET was designated to validate the accuracy of the CZCS radiometric measurements and to connect the instrument's measurements to standard measures of oceanic biological productivity and optical seawater clarity. In the period following the cessation of CZCS observations, some of the insight and experience gained by the CZCS NET activity has dissipated as several proposed follow-on sensors failed to achieve active status. The Sea WiFS mission will be the first dedicated orbital successor to CZCS it in turn precedes observations by the Moderate Resolution Imaging Spectroradiometer (MODIS) of the Earth Observing System (EOS). Since the CZCS NET experience is an important model for Sea WiFS and MODIS surface truth efforts, this document is intended to provide a comprehensive review of the validation of oceanographic data for the first orbital ocean color sensor mission. This document also summarizes the history of the CZCS NET activities. The references listed in the Bibliography are a listing of published scientific research which relied upon the CZCS BET algorithms, or research which was conducted on the basis of CZCS mission elements

Ocean surface provinces off Southwest Iberia based on satellite remote sensing

This thesis aimed to partition the complex surface marine domain off Southwest Iberia Peninsula (SWIP), using satellite remote sensing, and use it to assess phytoplankton variability patterns and underlying environmental drivers (1997 – 2015). Three unsupervised partition strategies, based on distinct input databases and temporal representations, detected a variable number of partition units (regions, provinces) of singular environmental and phytoplankton patterns within SWIP. An abiotic-based partition delineated 12 dynamic Environmental Provinces (EPs) that alternated coverage dominance along the annual cycle. EP patterns were in general related to phytoplankton biomass, indicated by satellite chlorophyll-a concentration (Chl-a), and productivity, thus supporting the biological relevance of this abiotic-based partition. A static partition, based on the main variability modes of Chl-a, derived 9 Chl-a regions. Moreover, a static partition strategy synthesised phytoplankton phenological patterns over SWIP into 5 phenoregions, with coherent patterns of timing, magnitude and duration of blooms. The spatial distribution of EPs, Chl-a regions and phenoregions shared similarities, which can be considered the main spatial patterns of SWIP ocean surface. In general, the spatial arrangement of the partition units showed a separation between coastal and open ocean, a latitudinal division (ca. 36.5oN) over the open ocean and, over the coast and slope, the influence of coastal upwelling along the west Portuguese coast and Cape São Vicente, and of river discharge along the northeastern Gulf of Cadiz. The environmental drivers of phytoplankton varied across partition units. Water column stratification, riverine discharge and upwelling intensity were the most influential modulators, and large scale climate indices usually showed minor effects. Environmental variables, Chl-a and phenology showed significant seasonal variability patterns, varying across regions. Interannual patterns were more complex, and significant trends were mostly detected within the Gulf of Cadiz. Linkages between environmental variability and phytoplankton support their use as an indicator of ecosystem status and change.O oceano superficial é um domínio extremamente complexo e dinâmico, onde as interações com a atmosfera e o continente modulam a distribuição e atividade dos organismos marinhos e o clima da Terra. O fitoplâncton, principal produtor primário marinho, é fortemente influenciado pelos processos atuantes no oceano superficial, constituindo um importante indicador do estado e variabilidade dos ecossistemas marinhos. Assim, a organização espacial horizontal do oceano superficial, função da variabilidade das propriedades abióticas e comunidades biológicas (incluindo o fitoplâncton), apresenta uma série de unidades funcionais distintas (regiões ou províncias), com atributos e padrões de variabilidade específicos. A partição ou regionalização do oceano, com identificação e delimitação destas unidades funcionais, simplifica a complexidade do oceano superficial e representa uma ferramenta para avaliar e compreender o funcionamento do oceano superficial, apresentando diversas aplicações ao nível do estudo, gestão e conservação dos ecossistemas marinhos. A deteção remota por satélite constitui uma fonte valiosa de dados para a partição do oceano superficial, pois disponibiliza campos sinóticos de várias variáveis oceanográficas e atmosféricas, em escalas espacial e temporal pertinentes, abrangendo períodos de várias décadas. A presente tese pretende particionar o complexo domínio marinho superficial do sudoeste da Península Ibérica (Southwest Iberia Peninsula, SWIP), com base em deteção remota por satélite, e avaliar a variabilidade do fitoplâncton e forçadores ambientais associados em regiões específicas (unidades funcionais) da área de estudo. Para atingir os objectivos principais foi inicialmente efetuada uma revisão do conhecimento científico sobre as estratégias de partição do oceano superficial baseadas em deteção remota por satélite (Capítulo 2) e, posteriormente, foram aplicadas diversas estratégias de partição nãosupervisionadas à área de estudo (Capítulos 3 - 5). Tais estratégias permitiram particionar a área de estudo com base em diferentes caraterísticas do oceano superficial (propriedades abióticas, variação da concentração de clorofila-a e índices fenológicos do fitoplâncton) e diferentes abordagens metodológicas (métodos de partição e resolução temporal). As diferentes partições do SWIP foram utilizadas para avaliar os padrões de variabilidade da biomassa e fenologia do fitoplâncton e suas relações com diferentes forçantes ambientais. No contexto deste estudo, as variáveis ambientais avaliadas incluíram variáveis locais indicadoras do ambiente físico, químico e ótico, variáveis hidrológicas indicadoras de processos costeiros (descarga dos rios e intensidade do afloramento costeiro) e indicadores climáticos de larga escala.This thesis was supported by Science without Borders Programme from the Brazilian National Council for Scientific and Technological Development (237998/2012‐2