Chromophoric dissolved organic matter (CDOM) is a part of total dissolved organic matter (DOM), playing an important role in marine carbon cycling. Thus, a better description of the fates of DOM may increase our understanding of DOM sources and sinks in the coastal zone. This study aims to explore the distributions, transformation and transport of CDOM in the Kaoping Estuary-Canyon system. The water exchange time (£n) of Kaoping estuarine water ranged from 0.1 to 2.2 day, being much shorter in the wet season than in the dry season. The riverine materials may be flushed out of the estuary without significant transformation in the estuary during the wet season, thus, distributions of nutrients and dissolved organic carbon(DOC) were largely determined by the mixing process. However, distributions of materials may be controlled by biogeochemical processes during the dry season, due to longer water residence time. In early spring, higher temperature and longer water residence time may be responsible for the effective decay of organic matter and nitrate reduction and/or denitrification in the estuary. Nonconcervative distribution (addition) of protein-like CDOM in early spring appeared to be derived from biological and/or sewage sources. In the wet season, the distribution of terrestrial humic-like CDOM was not only controlled by the conservative mixing between river water and coastal water, but also influenced by a release from total suspended matter (TSM). In the dry season, the CDOM was slightly removed from the photobleaching process occurring around the river mouth, which may be regarded as the major sink process of CDOM. In the Kaoping Canyon, the addition of terrestrial humic-like CDOM from TSM resuspension is significant only in the deep water. The photobleaching reaction occurred only in the limited area during the dry season, and gave little impact on CDOM concentration. There were no significant in-situ addition and removal in the coastal surface waters suggesting that the terrestrial humic-like CDOM could be a conservative tracer of terrestrial DOM in the coastal zone. The terrestrial inputs of DOM may play a minor role in determining distributions of protein-like CDOM in the Kaoping Canyon. On the contrary, distributions were primarily controlled by biological sources. Nutrient inputs from the Kaoping River may be responsible for increasing the primary production in the surface water of coastal zone, linking to a potential source of protein-like CDOM. Significant correlations were found between DOC and tryptophan for those surface waters with higher fluorescence intensity. The results suggested that tryptophan may be derived from biological origins. DOC released from phytoplanktons generally contains lower Tyrosine/Tryptophan ratio than that released from microbes. The Tyrosine/Tryptophan ratio may be used as an indicator for the condition of microbial community.

Surface waters receive large amounts of dissolved organic matter (DOM) via runoff from land. The DOM is rich in organic carbon that serves as an energy source for the aquatic biota. During uptake of this energy, aquatic organisms mineralize organic carbon. The resulting inorganic carbon is partially released to the atmosphere as carbon dioxide and methane that are greenhouse gases, and which are of concern for the ongoing global warming. The rate at which organic carbon is mineralized depends strongly on DOM quantity and quality that vary with respect to both time and space. In this thesis, DOM quantity and quality were addressed using spectroscopic methods that build on the absorptive and fluorescent properties of chromophoric DOM (CDOM). New techniques to measure CDOM absorption and fluorescence were applied and further developed that allowed us to present novel CDOM variability patterns. Addressing the lake-rich Scandinavian landscape, strong focus was placed on water retention by lakes that tightly links to lake DOM quantity and quality. An analysis of 24,742 lakes from seven large Swedish river systems indicated that the majority of lakes in Sweden exchange their water within one year. From headwaters to the Sea, summed lake volumes in the catchments of lakes were found to increase at rates comparable to discharge, which indicated effective water renewal along flow. A strong relationship between lake water retention and CDOM was apparent and further investigated based on samples from a lake district to a regional scale. Results from in situ high-frequency monitoring of CDOM absorption in a eutrophic humic lake showed intra-annual variability patterns known from oligotrophic lake systems. The patterns for CDOM absorption contrasted results obtained for synchronously measured partial pressures of carbon dioxide that showed diurnal signals. Measurements of CDOM fluorescence and DOC concentrations indicated lake-internal DOM production. A comparison of these results with results from addressing 560 lakes distributed across Sweden, showed that a well-calibrated CDOM fluorescence measurement captures signals from lake-internal DOM production. I conclude that improved CDOM fluorescence measurements are promising to address lake-internally produced DOM.

Chromophoric Dissolved Organic Matter (CDOM) is a substance produced by the planktonic community that naturally blocks biologically damaging, ultraviolet radiation (UV; wavelengths = 280 to 400 nm). While a variety of planktonic species produce CDOM, investigations into the quality and quantity of their CDOM production are few. The purpose of this study was to investigate the properties of CDOM produced by phytoplankton versus zooplankton. Typically, UV radiation breaks down CDOM. However, marine organisms sometimes produce CDOM that, when exposed to sunlight, increases its absorbance of UV radiation. The reasons for this anomaly and the source of this unusual CDOM are unclear. To test for distinctions among sources, filtered water samples from cultures of two marine phytoplankton, Gymnodinium sp. and Dunaliella sp., and a marine copepod, Tigriopus californicus were exposed to sunlight for intervals of 0, 0.5, 1, 2, and 4 hours. The maximal UVB radiation (wavelengths; λ = 280 to 320 nm) was 0.1699 J cm-2. Before and after sunlight exposures, CDOM sources were assessed by comparing absorbance spectra from 184 to 730 nm with detailed comparisons at wavelengths of 254, 305, 320, and 350 nm. Results are expressed as "absorption", which is the raw absorbance converted to the natural log. Before exposure to sunlight, CDOM from algal species had 5- to 8-times higher average absorption values across UV wavelengths than CDOM produced by Tigriopus. CDOM samples produced by phytoplankton were more susceptible to photochemical change than CDOM from Tigriopus. In response to sunlight, CDOM from Gymnodinium varied greatly, increasing in UV absorption in 2 out of 5 replicates but decreasing in absorption in the other replicates. In contrast, peak absorption at λ = 260 nm of CDOM from Dunaliella decreased directionally by an average of 76% in absorption and 75% in specific absorption, and this decrease in absorption was significant (p = 0.03). CDOM from Tigriopus significantly decreased in both absorption (all UV wavelengths, p < 0.01) and "specific absorption", which is absorption standardized per mg of dissolved organic carbon (λ = 320 nm; p < 0.03), but the magnitude of change was only 17%. Thus, photochemical responses of CDOM from the three planktonic sources demonstrated more, consistently less, and unchanged UV absorption. Phytoplankton biomass, which is greater than that of copepods at the next trophic level, likely produce more CDOM but because of greater variability in CDOM absorbance of UV both within and between algal sources, copepods may offer a more stable source of UV protection depending on sunlight exposure and their relative abundance. Definitive conclusions depend on future laboratory studies expanded to more planktonic organisms as well as in situ studies during oceanographic cruises to test the relative contributions of planktonic species.

Le lagon de la Nouvelle Calédonie (Pacifique Sud-Ouest), est drainé par les entrées fluviales et océaniques sous la pression de l’érosion des sols ultramafiques (enrichies en Nickel et Cobalt). Le but de cette thèse était de mieux comprendre les sources et la variabilité spatio-temporelle de la matière organique dissoute colorée (MODC) et fluorescente (MODF) le long de continuum rivière-côte-lagon-large en zone lagonaire tropicale du Pacifique dans un contexte de changement climatique et d’anthropisation locale (activité minière). Les côtes Est et Ouest calédoniennes ont été échantillonnées pendant 1 an et demi et pendant la campagne CALIOPE 3 (côte Est) lors d’un épisode El Niño fort (2015-2016), ponctués de forts épisodes pluvieux. L’analyse parallèle factorielle (PARAFAC) des matrices d’excitation-émission de fluorescence (MEEFs) a abouti à l’indentifications de 5 fluorophores : humique-like marin, 2 tyrosine-like, et tryptophane-like d’origine autochtone issus des compartiments phytoplanctoniques et bactériens, et un fluorophore humique-like d’origine allochtone provenant des rivières drainant les côtes. La MODC à 350 et 442 nm suivait une dynamique fortement dépendante des apports fluviaux pouvant être découplée de la dynamique de la MODF. La MODF sur la côte Est suivait un cycle saisonnier (saison sèche/humide) contrairement à la côte Ouest dépendante de d'évènements pluvieux sporadiques. Des fluorophores (humique, tyrosine et tryptophane-like) ont montré des affinités avec certains métaux traces (Nickel, Manganèse, Cobalt) ce qui a permis de développer une expérience de quenching de fluorescence pour déterminer le pouvoir complexant de la MODF naturelle. / New Caledonia (South-West Pacific) is a tropical area under strong environmental pressure (climate change and local anthropogenic forcing). The aim of this thesis was to gain a better understanding of the colored (CDOM) and fluorescent (FDOM) dissolved organic matter dynamic in the New Caledonia Lagoon where strong ultramafic erosion pressure is associated with trace metals (i.e., nickel, manganese and cobalt). 3D spectrofluorimetry was used to characterize the CDOM/FDOM. The West and East coasts were sampled during one year and a half in a context of El Niño (2015-2016), interrupted by strong rainy events (storms) and during CALIOPE 3 cruise (East coast). A parallel factor analysis (PARAFAC) of EEMF led to the identification of 5 fluorophores: marine humic-like, 2 tyrosine-like and tryptophan-like peaks (T2 peak) from the biological balance between phytoplankton and bacterioplankton and a terrestrial humic-like from rivers draining caledonian coast. The CDOM signal at 350 and 442 nm had a strong dependency on river inputs accentuated during storms and revealed photodegraded CDOM. The FDOM signal in the East showed a seasonal cycle (wet/dry season) contrary to the West coast depending on sporadic rainy events. Data acquired during the CALIOPE 3 were coupled with trace metal concentrations, biogeochemical parameters, and plankton communities. Some fluorophores displayed a preferential association with nickel and cobalt. The complexation capacities of these fluorophores toward trace metals were revealed by a quenching experiment that allowed to derive complexation constants.

Given the pace of climate change in the Arctic, it is vital to better constrain terrigenous dissolved organic matter (tDOM) fluctuations in large Arctic Rivers and the role that climate change may bring to tDOM inputs into the Arctic Ocean and to the global carbon cycle. This project uses the optical properties of chromophoric dissolved organic matter (CDOM) to investigate the quality, quantity and fate of dissolved organic matter (DOM) in large Arctic Rivers and the interior Arctic Basin. In large rivers surrounding the Arctic, peak discharge CDOM is largely derived from fresh terrestrial plant material whereas during base flow the CDOM pool has a greater microbial imprint, particularly in the Mackenzie. The higher microbial imprint in the Mackenzie can be explained by longer water residence times, which may be important in a warming climate where increased precipitation rates will likely lead to increased hydrological connectivity and therefore longer water residence times. In surface waters of the Canadian Archipelago, 17 % of the DOM pool is of terrestrial origin, even though waters are diluted with sea ice melt, suggesting the likelihood of a subsurface plume of tDOM entrained within river runoff from Arctic Rivers. In the interior Arctic, an elevated terrestrial CDOM signal in the Eurasian Basin (EB) points to the presence of Eurasian river CDOM entrained within river runoff in the Transpolar Drift. In contrast, autochthonous/microbial CDOM sources become more important the Canadian Basin (CB) and the terrestrial CDOM signal is much lower relative to the EB. A good constraint on the nature and distributions of freshwater (FW) in the Arctic Ocean is paramount to understand the role climate change may play for the Arctic’s hydrological cycle. During this study, we used the spatial patterns of terrestrially derived CDOM to better understand the distribution and nature of river runoff across the upper Arctic Basin. This study illustrates the usefulness of CDOM to finger-print water masses within the Arctic Ocean and shows promise to improve our understanding of upper Arctic Ocean ventilation patterns.

Afin de comprendre, caractériser et prédire l’évolution des cycles biogéochimiques océaniques face au changement climatique global, il est nécessaire d’appréhender au mieux la dynamique de la matière organique (MO) au niveau des interfaces « terre/océan ». Dans ce contexte, l’objectif général de cette thèse était d’améliorer les connaissances sur la dynamique de la fraction dissoute chromophorique de la MO (CDOM) des eaux de surface côtières méditerranéennes et arctiques, et d’en déterminer l’impact sur l’atténuation du rayonnement UV (UVR) et visible (PAR) sous-marin. Pour cela, l’étude des propriétés optiques d’absorbance et de fluorescence de la CDOM, couplée à des mesures radiométriques atmosphériques et sous-marines, ont été réalisées lors d’un cycle saisonnier en Baie de Marseille (station SOFCOM), et lors d’une mission océanographique en Mer de Beaufort durant l’été 2009. La Baie de Marseille est caractérisée par des quantités de CDOM faibles (aCDOM(350) = 0,10 ± 0,02 m-1), particulièrement à la fin de la période estivale de stratification, à cause de l’intensité de l’éclairement solaire, enrichi en UVR-B, qui dégrade et blanchie cette CDOM (SCDOM = 0,023 ± 0,003 nm-1). Dans cette zone côtière fortement urbanisée, la dynamique de la CDOM est pilotée par des processus biotiques (production biologique in situ et induite par les intrusions épisodiques du panache du Rhône) et abiotiques (photo-blanchiment et brassage). La CDOM est essentiellement d’origine autochtone, même lors d’événements d’intrusion du panache du Rhône (photo-dégradation de la CDOM terrestre durant son transit). Lors des périodes d’efflorescences algales, la CDOM se compose principalement de matériel récent, de type protéique (pic T), qui absorbe préférentiellement les courts UVR. Ces pulses de CDOM récente se superposent à un persistent signal de fond de CDOM composé majoritairement de matériel âgé, de type humique (pics M et C), qui absorbe les UVR et également le PAR. Au niveau du plateau Canadien de la Mer de Beaufort, la CDOM est très abondante (aCDOMmax(350) = 6,36 m-1), fortement influencée par les apports allochtones du Mackenzie (pics A-C et M) et décroit de manière conservatrice avec la salinité. Dans les eaux marines (salinité >25), la CDOM, qui présente de plus faibles concentrations (aCDOM(350) = 0,21 ± 0,13 m-1), provient d’une production biologique in situ récente favorisée par des upwellings ainsi que d’injections de CDOM (pics B-T et M) lors de la formation/fonte de la glace de mer. Etonnamment, la source principale du composé « humique marin » (pic M) n’est pas autochtone. Elle est issue d’apports allochtones provenant du Mackenzie. Celui-ci draine en effet de nombreux lacs qui sont le siège d’une intense activité biologique, et il est proposé dans cette thèse que les macrophytes qui s’y développent seraient à l’origine du pic M. Cette source de CDOM biologique allochtone, couplée aux processus de photo-blanchiment et d’absorption sur les particules de la CDOM terrestre, pourraient expliquer les valeurs élevées de SCDOM (&#8776; 0,020 nm-1) du Mackenzie en été. / To understand, characterize, and predict the evolution of oceanic biogeochemical cycles in relation to the global climate change, it is necessary to better understand the dynamics of organic matter (OM). In this context, the overall objective of this thesis was to get more insights chromophoric dissolved fraction of OM (CDOM) dynamics in surface Mediterranean and Arctic coastal waters and to determine the impact on attenuation of ultraviolet (UVR) and visible (PAR) underwater radiation. For this, the study of optical properties of absorbance and fluorescence of CDOM, coupled with atmospheric and underwater radiometric measurements, were made during a seasonal cycle in the Bay of Marseille (SOFCOM station), and in the Beaufort Sea during summer 2009. The Bay of Marseilles is characterized by low amounts of CDOM (aCDOM(350) = 0.10 ± 0.02 m-1), particularly in end summer stratification period due to the intensity of the solar irradiance, enriched in UVR-B, which degrades and bleaches CDOM (SCDOM = 0.023 ± 0.003 nm-1). In this highly urbanized coastal area, the dynamics of CDOM are driven by biotic processes (in situ biological production and within the Rhône River plume) and abiotic (photo-bleaching and mixing). Our results showed that CDOM is mostly of autochthonous origin, even during Rhône plume intrusion events (photo-degradation of terrestrial CDOM during the transit). During bloom periods, the CDOM consists mainly of a recent type protein (peak T), which preferentially absorbs in the short UVR. These pulses of recent CDOM are superimposed on a persistent background of CDOM mainly composed of aged material, humic-type (peaks M and C), which absorbs UVR and PAR. Over the Canadian shelf of the Beaufort Sea, CDOM is highly abundant (aCDOMmax (350) = 6.36 m-1) and strongly influenced by allochthonous inputs from the Mackenzie (peaks A-C and M) decreasing conservatively with salinity. In marine waters (salinity> 25), CDOM had lower concentrations (aCDOM(350) = 0.21 ± 0.13 m-1) and originated from a recent in situ biological production favored by upwelling and brine injections (peaks B-T and M). Surprisingly, the main source of the marine humic-like component (peak M) was not autochthonous. This material originates from allochthonous inputs from the Mackenzie River, which traverses numerous lakes where intense biological activity occurs. We suggest that this activity is mainly due to the macrophytes development, which may in part explain the origin of the peak M. This source of organic allochthonous CDOM coupled to other processes such as photobleaching and absorption on the particles of terrestrial CDOM, could explain the high values of SCDOM (&#8776; 0.020 nm-1) recorded in the Mackenzie during summertime.

In situ measurements were used to study the bio-optical properties of marine waters within the Gulf of Paria (GOP, Venezuela) and in the Southeastern Caribbean Sea (SEC) as they are affected by the seasonal discharge of the Orinoco River plume. The main purpose of this study was to determine the impact of colored dissolved organic matter (CDOM) (also known as Gelbstoff), phytoplankton, and total suspended matter (TSM) in the color of the Orinoco River plume. This information is essential for regional ocean color algorithms development. Salinity and silica values indicate that the GOP and SEC waters were under the influence of the Orinoco River plume during both seasons. This riverine influence resulted in high values of Gelbstoff absorption, αg(λ), which contributed to up to 90% of the total absorption at 440 nm in both the GOP and SEC regardless of the season. Phytoplankton absorption contributions were normally around 5%, but during the dry season these values reached 20% in the SEC. Ratios of αg(440) to αph(440) were extremely large, with most of the values ranging from 10 to 50. Due to the strong absorption by Gelbstoff, light at the blue wavelengths (412 nm, 440 nm and 490 nm) was attenuated to 1% of the subsurface irradiance in the first 5 m of the water column within the GOP, and in the first 10 m of the water column in the SEC. Furthermore, the absorption by Gelbstoff significantly decreased the water leaving radiance (Lw(λ)) in the blue wavelengths along the Orinoco River plume. As αg(λ) relatively decreased from the GOP to the SEC (X≈1.6 m-1 and X≈ 0.9 m-1, respectively), a shift in the maximum peak of Rrs(λ) spectra (Rrsmax(λ)), towards shorter wavelengths (from ~ 580 nm to ~500 nm) was observed. Similar to Gelbstoff, concentrations of TSM normally decreased from the stations near the Delta to the stations in the SEC. The impact of TSM on the color of the Orinoco plume was represented by a reduction in the magnitude of Rrsmax(λ) of ~50% going from the waters near the Orinoco delta to the SEC, indistinctively of the season.

A dual wavelength method was developed for the field detection of optical brighteners (OBs), fluorescent laundry additives used as indicators of anthropogenic wastes. The method was quantitative for OBs under variable levels of fluorescent colored dissolved organic matter (CDOM). Based on excitation at 300-400 nm and 440 and 550 nm emission, the method assumed a constant ratio of fluorescence due to CDOM alone, even if absolute amplitude varied. Concentrations of OBs were computed as the difference between the observed 440 nm emission and the expected CDOM fluorescence at 440 nm, as extrapolated from the 550 nm fluorescence and established CDOM fluorescence ratio. Real-time inner filter corrections were based on absorption modeled from 550 nm fluorescence and from exponential relationships at alternate wavelengths. The effects of temperature and dissolved oxygen on CDOM fluorescence and computed OB were quantified but were minimal because effects were comparable between the two fluorescence regions. Assumptions on the locally conservative behavior of CDOM were supported in field surveys of sewered and non-sewered areas. Varying water masses were detected, but OB quantities were detected that did not co-vary with fluorescence alone. Eleven geographic regions of peninsular Florida and sources of OBs were sampled to evaluate the method under a broader range of CDOM and to conduct an extensive detergent spike analysis. Fluorescence data were collected as EEMs and subjected to PARAFAC modeling, isolating eight spectral factors that could sufficiently describe all samples. There were no visible regions of the spectra that were unique to detergents or OBs, but a previously unreported peak in the UV (<230 / 284 ex / em) was tentatively identified as a detergent surfactant and should be pursued as a potential complementary indicator of anthropogenic wastes. Limits on EEM fluorescence measurements were identified: maximum linear range, maximum turbidity, and sensitivity to assumptions. A sub-sampling technique of EEM data approximated the filter fluorometer readings, was used to optimize the dual wavelength method, validated the method with spike recoveries, and presented alternative approaches.

The variability of water-column absorption due to colored dissolved organic matter (CDOM) and phytoplankton in coral reef regions is the focus of this study. Hydrographic and CDOM absorption measurements made on the Bahamas Banks and in Exuma Sound during the spring of 1999 and 2000 showed that values of salinity and CDOM absorption at 440nm were higher on the banks (37.18 psu, 0.06 m^-1), compared to Exuma Sound (37.04 psu, 0.03 m^-1). Spatial patterns of CDOM absorption in Exuma Sound revealed that plumes of CDOM-rich water flow into Exuma Sound from the surrounding banks. To examine absorption variability in reef regions throughout the world, a thirteen-year time series of satellite-derived estimates of water-column absorption due to CDOM and phytoplankton were created from Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate Resolution Imaging Spectroradiometer (MODIS) data. Time series data extracted adjacent to coral reef regions showed that variability in absorption depends on oceanographic conditions such as circulation patterns and winds as well as proximity to sources of light-absorbing materials that enter the water column, such as from terrestrial runoff. Waters near reef regions are generally clear, exhibiting a lower "baseline" level of CDOM absorption of approximately 0.01 m^-1 at 443nm. The main differences between regions lie in the periods during the year when increased levels of absorption are observed, which can be triggered by inputs of terrestrially-derived material, as in the Great Barrier Reef lagoon, or wind-driven upwelling as in the Andaman Sea and eastern Pacific Ocean near Panama. The lowest CDOM absorption levels found were approximately 0.003 m^-1 at 443nm near the islands of Palau and Yap, which are removed from sources of colored materials. The highest absorption levels near reefs were associated with wind-driven upwelling during the northeast monsoon on the Andaman coast of Thailand where values of CDOM absorption at 443nm reached 0.7 m^-1. Simulations of the underwater light field based on satellite-derived absorption values revealed that changes in absorption have a strong influence on light levels to which corals are exposed, particularly in the ultraviolet region of the spectrum, where CDOM is the primary absorber of light. Episodes of coral bleaching during 1998 and 2002 were found to be associated with elevated seawater temperatures as well as decreased levels of CDOM absorption, indicating that corals were exposed to light stress along with thermal stress during periods of bleaching.

In the northern Gulf of Mexico, hypoxia occurs annually during the summer on the Texas-Louisiana shelf. This study examines the distribution of particulate and dissolved components relative to hydrography, to better understand the processes controlling the development of hypoxia. Particulate matter on the Texas-Louisiana Shelf has three major sources – river plumes, primary production, and resuspended sediments. The sources and processes controlling distribution and transport of particles are investigated using optical proxies (backscattering, chlorophyll fluorescence, Colored Dissolved Organic Matter fluorescence (CDOM)), temperature, salinity, dissolved oxygen (DO), and in-situ sampling during June and August 2011 cruises of the Mechanisms Controlling Hypoxia program (hypoxia.tamu.edu). Discrete samples of particulate matter (PM) and particulate organic carbon (POC) concentration were obtained for analysis and calibration of optical instruments interfaced with a profiling CTD, a towed undulating CTD (Acrobat), and the ship’s flow-through system along the shelf from south of Galveston, Texas, to east of the Mississippi delta. The results of this study support a previously hypothesized concept of three primary areas of organic and inorganic particle composition and processes that dominate those areas – river-dominated water, highly productive surface waters, and clear, nutrient-poor low-productivity surface waters. The distribution and bulk composition of particulate matter in the northern Gulf of Mexico, plus the distribution of chlorophyll fluorescence and CDOM suggest that subpycnocline primary production plays a role in determining oxygen concentration in subpycnocline waters away from the river-dominated water.