Feeding of benthic foraminifera on diatoms and sewage-derived organic matter: an experimental application of lipid biomarker techniques

Foraminiferal ecology at sewage outfalls has been investigated in numerous field studies over the last 30 years. Foraminifera have been frequently used as biomonitors of sewage pollution since they are both abundant and ubiquitous. Sewage outfalls have been demonstrated to have both positive and negative effects on adjacent foraminiferal populations, but it has never been shown conclusively why sewage affects foraminifera in these ways. Such information on the impact mechanisms of sewage pollution is essential if foraminifera are to be used as sewage pollution biomonitors, and also to understand the ecology of these important protists. One possible cause of a positive effect is the direct consumption of sewage-derived particulate organic matter (POM) by the foraminifera themselves. However this hypothesis has never been tested experimentally. Here, lipid (fatty acid and sterol) biomarker techniques were applied to study the ingestion of two potential food items by the foraminiferan Haynesina germanica in the laboratory. An experiment was conducted to confirm that the laboratory conditions were conducive to the survival and feeding of the foraminifera. In this experiment, foraminifera were provided with the pennate diatom Phaeodactylum tricornutum, which was considered to be a suitable food source. After 2 weeks, a four-fold increase in the levels of the diatom fatty acid biomarker, 20:5(n-3), in the foraminifera suggested that they had fed actively on the diatoms and survived under the experimental conditions. These experimental conditions were used in the main experiment, where foraminifera were fed the POM from sewage. Lipid biomarker analysis indicated that H. germanica did not consume secondary treated sewage-derived POM. Neither fatty acid profiles in the sewage nor coprostanol, the diagnostic human faecal sterol, were detected in foraminifera after exposure to the potential sewage food source. However, foraminifera may have consumed bacteria associated with the sewage in the experiment. The findings are discussed in terms of current EU legislation on sewage treatment that has affected the composition of sewage discharges, and therefore possibly reduced the nutritive value of sewage to the marine benthos.     

Total Lipid and Fatty Acid Classes in Decomposing Mangrove Leaves of <Emphasis Type="Italic">Bruguiera gymnorrhiza</Emphasis> and <Emphasis Type="Italic">Kandelia candel</Emphasis>: Significance with respect to Lipid Input

Changes in the concentration of total lipid and fatty acids (FAs) during the decomposition of mangrove leaves were investigated by field experiments using yellow leaves of Bruguiera gymnorrhiza (L.) Lamk. and Kandelia candel (L.) Druce, in order to quantify mangrove contribution to lipid and fatty acid inputs to marine sediments. Total lipid and total FA in the fresh (green and yellow) and decomposing leaves of both species were significantly higher during winter than summer. During decomposition, total lipid content and FA concentration, in particular branched chain fatty acids (BrFAs) and bacterial fatty acids (BFAs), increased to a maximum concentration in 45 days during winter and in 17 days during summer. Lipids were lost faster in K. candel leaf detritus than in B. gymnorrhiza leaf detritus in which >90% of the total lipid original weight was lost during the summer experiment and <60% during the winter experiment. The changes in the concentrations of total lipids and FAs in the decomposing leaves also indicate that mangrove leaves are significant sources of fatty acids and probably other lipid compounds to estuarine ecosystems and that tidal waters transport the lipids and FAs adsorbed to particulate matter from mangroves to adjacent estuarine sediments and the ocean.     

Trace element and molecular markers of organic carbon dynamics along a shelf–basin continuum in sediments of the western Arctic Ocean

Molecular organic biomarkers together with trace element composition were investigated in sediments east of Barrow Canyon in the western Arctic Ocean to determine sources and recycling of organic carbon in a continuum from the shelf to the basin. Algal biomarkers (polyunsaturated and short-chain saturated fatty acids, 24-methylcholesta-5,24(28)-dien-3β-ol, dinosterol) highlight the substantial contribution of organic matter from water column and sea-ice primary productivity in shelf environments, while redox markers such as acid volatile sulfide (AVS), Mn, and Re indicate intense metabolism of this material leading to sediment anoxia. Shelf sediments also receive considerable inputs from terrestrial organic carbon, with biomarker composition suggesting the presence of multiple pools of terrestrial organic matter segregated by age/lability or hydrodynamic sorting. Sedimentary metabolism was not as intense in slope sediments as on the shelf; however, sufficient labile organic matter is present to create suboxic and anoxic conditions, at least intermittently, as organic matter is focused towards the slope. Basin sediments also showed evidence for episodic delivery of labile organic carbon inputs despite the strong physical controls of water depth and sea-ice cover. Principal components analysis of the lipid biomarker data was used to estimate fractions of preserved recalcitrant (of terrestrial origin) and labile (of marine origin) organic matter in the sediments, with ranges of 12–79%, 14–45%, and 37–66% found for the shelf, slope, and basin cores, respectively. On average, the relative preserved terrestrial organic matter in basin sediments was 56%, suggesting exchange of organic carbon between nearshore and basin environments in the western Arctic.     

Assessment of the effects of hydrocarbon contamination on the sedimentary bacterial communities and determination of the polar lipid fraction purity: Relevance of intact phospholipid analysis

This in situ study reports on the relevance of intact phospholipids as new biomarkers and highlights the limits of the classical fatty acid analysis after the hydrolysis of the polar lipid fraction. The analysis of polar lipid fractions revealed significant contributions of marine macrophytes with either non-phospholipid compounds (sulfoquinovosyl diacylglycerol) or with both non-bacterial phospholipid classes (phosphatidylcholine) and non-bacterial phospholipid molecular species (some molecular species of phosphatidylglycerol). The analysis of intact phospholipids showed also the predominance of gram-negative bacteria in sediments whereas the analysis of fatty acids alone cannot confirm such information. Lastly, as regard to the effects of petroleum hydrocarbons on the sedimentary bacterial communities, we observed a higher degree of saturation of the fatty acyl chains of the phospholipids extracted from sediment exposed to a massive and chronic crude oil contamination. Such a result was interpreted as an adaptive response resulting in higher membrane rigidity of the bacterial communities.     

脂类生物标志物在海洋环境中的应用与研究进展

海洋沉积物中的脂类生物标志物可以提供丰富的信息,包括有机物质源,沉积过程的古环境条件等。由于脂类生物标志物提供的信息准确、稳定,成为研究海洋环境的有力工具。本文介绍了其在古气候效应、河口系统的有机物质检测、降解以及污染物溯源的研究应用进展。     

Lipid biomarkers for anaerobic oxidation of methane and sulphate reduction in cold seep sediments of Nyegga pockmarks (Norwegian margin): discrepancies in contents and carbon isotope signatures

Distributions and carbon isotopic compositions of microbial lipid biomarkers were investigated in sediment cores from the G11 and G12 pockmarks in the Nyegga sector of the Storegga Slide on the mid-Norwegian margin to explore differences in depth zonation, type and carbon assimilation mode of anaerobic methane-oxidizing archaea (ANMEs) and associated sulphate-reducing bacteria responsible for anaerobic oxidation of methane (AOM) in these cold seep environments. While the G11 site is characterised by black reduced sediments colonized by gastropods and Siboglinidae tubeworms, the G12 site has black reduced sediments devoid of fauna but surrounded by a peripheral occurrence of gastropods and white filamentous microbial mats. At both sites, bulk sediments contained abundant archaeal and bacterial lipid biomarkers substantially depleted in ¹³C, consisting mainly of isoprenoidal hydrocarbons and dialkyl glycerol diethers, fatty acids and non-isoprenoidal monoalkylglycerol ethers. At the G11 site, down-core profiles revealed that lipid biomarkers were in maximum abundance from 10 cm depth to the core bottom at 16 cm depth, associated with δ¹³C values of ?57 to ?136‰. At the G12 site, by contrast, lipid biomarkers were in high abundance in the upper 5 cm sediment layer, associated with δ¹³C values of ?43 to ?133‰. This suggests that, as expected from the benthic fauna characteristics of the sites, AOM takes place mainly at depth in the G11 pockmark but just below the seafloor in the G12 pockmark. These patterns can be explained largely by variable fluid flow rates. Furthermore, at both sites, a dominance of ANME-2 archaea accompanied by their bacterial partners is inferred based on lipid biomarker distributions and carbon isotope signatures, which is in agreement with recently published DNA analyses for the G11 pockmark. However, the present data reveal high discrepancies in the contents and δ¹³C values for both archaeal and bacterial lipid profiles, implying the possible involvement of at least two distinct AOM-related microbial consortia at the inferred AOM depth zonation of G11 and G12 pockmark sediments. In both sediment cores, the δ¹³C profiles for most archaeal lipids suggest a direct assimilation of dissolved inorganic carbon (DIC) in addition to methane by ANMEs (chemoautotrophy); constant and highly depleted δ¹³C profiles for PMI:3, an archaeal lipid biomarker presumably related to ANME-2, suggest a direct assimilation of ¹³C-depleted methane-derived carbon via AOM (methanotrophy). Evidently, the common approach of investigating lipid biomarker contents and δ¹³C signatures in cold seep sediments does not suffice to precisely discriminate between the carbon assimilation mode for each ANME archaeal group and associated bacteria. Rather, this needs to be combined with further specific labelling studies including different carbon sources (methane carbon, methane-derived organic intermediates and DIC) in order to unravel the metabolic pathways of each microbial consortium involved in AOM (ANME-1 vs. ANME-2 vs. ANME-3 archaeal group and associated bacteria).     

Fatty acid composition of phytoplankton, settling particulate matter and sediments at a sheltered bivalve aquaculture site

Fatty acid biomarkers were used to investigate the biogeochemistry of a former blue mussel (Mytilus edulis) aquaculture site in a shallow, sheltered cove in northeastern Newfoundland. High levels of polyunsaturated fatty acids (PUFA) in net-tow and sediment trap samples indicated a substantial phytoplankton source of organic matter, and fluctuations in specific fatty acid biomarkers reflected the changing abundances of diatoms and dinoflagellates. In comparison, sediments contained very low levels of PUFA (<15%) and were dominated by terrestrial and bacterial markers. In a separate study, blue mussels were grown at this closed site, providing the opportunity to examine the relationship between lipid supply, as recorded by net-tow and trap samples, and bivalve requirements. The average plankton fatty acid composition throughout the year agreed well with that of the adult blue mussels, suggesting that fatty acids were provided in proportions very similar to the bivalves' requirements. The fatty acid composition of the blue mussels was typical of those collected elsewhere, with PUFA proportions near 50%. However, examination of fatty acid data of plankton sampled in other areas revealed that the plankton in the current study may have been unusual in providing fatty acids at levels required by the bivalves.     

Microbial community structure analysis of euxinic sediments using phospholipid fatty acid biomarkers

Microbial community structure in sediments, as determined by the phospholipid ester-linked fatty acid (PLFA) analysis, collected from Kojima Lake during summer and winter was described with reference to the environmental quality of the lake. A characteristic feature of the study area was the persistence of anoxia in summer and winter in the deeper area, and the sediments were under the reduced condition with high levels of sulfide, chemical oxygen demand, and low values of oxidation-reduction potential. PLFA profiles of the sediment were dominated by the saturated, branched and monounsaturated fatty acids. Small amounts (less than 5% of the total PLFA) of polyunsaturated fatty acids (biomarker fatty acids of microeukaryotes) and long chain fatty acids were detected in sediments. Total PLFA concentrations in sediments were higher in summer than in winter. Microbial community structure in the lake sediments was predominated by the prokaryotes, as evidenced from the larger amounts of bacterial biomarker fatty acids in the range of C₁₀ to C₂₀. The presence of signature fatty acids of sulfate reducing bacteria in sediments was consistent with the high levels of sulfide in the sediment and anoxic condition in the study area. PLFA showed significant differences in PLFA profiles between shallow and deeper areas, indicating the differences in the lipid contributing communities. However, no such a significant difference was observed between summer and winter.     

脂肪酸标志物在海洋生态系统营养关系研究中的应用

脂肪酸在食物链传递过程中相对保守,可以作为标志物示踪研究海洋生物间的营养关系.脂肪酸标志物属于营养学标志物的一种,是海洋生态系统营养关系研究中很有发展前景的分析方法之一.总结概括了目前国际上应用较广泛的脂肪酸标志及脂肪酸标志体系的建立过程、近年来脂肪酸标志物在海洋生态系统营养关系研究中的应用领域,展望了脂肪酸标志法的应...     

Lipid biomarker composition in surface sediments from the Carlsberg Ridge near the Tianxiu Hydrothermal Field

Hydrothermal venting has a profound effect on the chemical and biological properties of local and distal seawater and sediments. In this study, lipid biomarkers were analyzed to examine the potential influence of hydrothermal activity on the fate of organic matter(OM) in surface sediments around Tianxiu Hydrothermal Field in the Carlsberg Ridge(CR), Northwest Indian Ocean. By comparing the biomarker distributions of the samples with that of other typical hydrothermal sediments in the mid ocean ridge, it is shown that the location of the samples is not affected by the hydrothermal activity. The relatively low abundances of terrestrial n-alkyl lipids and riverine1,15-C32 diol suggested a minor contribution of terrigenous OM to the study area. The bacteria contributed predominantly to sedimentary marine OM; however, other marine source organisms, e.g., eukaryotes(i.e.,phytoplankton and fungi) could not be completely neglected. The marine-originated biomarkers showed significantly variable distributions between the two sediments, suggesting different dynamic physical and biogeochemical processes controlling the fate of marine OM. This study identified various diagnostic biomarkers(5,5-diethyl alkanes, diols and β-OH FAs), which may have significant environmental implications for future works in this region.     

Water column distribution of phospholipid-derived fatty acids of marine microorganisms in the Humboldt Current system off northern Chile

Suspended particulate matter samples from the oxygenated surface zone, the oxygen minimum zone, and the oxygenated deeper zone were collected from the upwelling area off Antofagasta in northern Chile during austral autumn (April 2001) to study the composition of microbial phospholipid-derived fatty acid methyl esters, using capillary gas chromatography-mass spectrometry. Whereas phytoplanktonic carbon dominated living organic matter near the coast, bacterial carbon was most abundant offshore. The biomarker distribution showed some differences between the depth levels sampled, such as the highest microbial abundance in the epipelagic zone represented by phytoplankton, especially diatoms, and a homogeneous distribution of bacterial biomarkers, with no indication of vertical segregation of functional groups as previously thought.     

Sterols as markers of sewage contamination in a tropical urban estuary (Guanabara Bay, Brazil): space–time variations

Guanabara Bay, located adjacent to Rio de Janeiro in Brazil, is highly contaminated by substances derived from domestic and industrial effluents as well as from agricultural runoff. In the present work, sedimentary coprostanol and other faecal sterols were used to investigate historical trends in sewage contamination. Sediment cores were collected from eight different (and characterized) locations in the bay and were sectioned into dated segments. Organic carbon was determined by dry combustion and sterols were separated and quantified by GC/MS. The space-distribution of organic carbon and faecal sterol concentrations generally coincided with the presence of known pollution sources. Concentrations of coprostanol as high as 40 μg g⁻¹ were found, indicating areas of severe sewage contamination. Faecal sterol ratios, commonly used as tools to investigate contamination in temperate environments, however, were found to have limited applicability to this tropical estuarine system, probably due to the influence of intensive primary production and microbial processes.     

Vertical and lateral transport of organic carbon and the carbon budget in Santa Monica Basin, California

The flux and compositions of solvent-extractable lipid fractions were measured in particulate matter collected periodically by moored sediment traps in the Santa Monica Basin from 1985–1988. The purpose was to assess the compositional changes during settling, the carbon dynamics in the basin and to estimate the impacts of energy-related by-products on the surface sediments. Sediment traps recorded consistently high lipid fluxes in the eastern slope relative to the central basin, reflecting elevated terrigenous carbon inputs possibly from land-based human activities. Generally, lipid fluxes decrease offshore but increase vertically with water depth below 500m, implying lateral transport of particles. The steep decline of flux in the top 500m of the water is related to the rapid decomposition and mineralization of the marine-derived cellular carbon compounds. Less than 5% of the marine lipid components reach the seabed. In contrast, preferential preservation of terrigenous lipid is clearly evident from the chemistry of deeper traps and surface sediments.The lateral transport of particles is reflected in the presence of higher plant-derived lignin phenols and sewage-derived coprostanol and epicoprostanol in the deep trap material as well as in surface sediment throughout the basin. Petroleum triterpanes characteristic of natural seepage also permeates through the entire basin. Based on the data collected from both the trap particulte matter and surface sediments, a carbon budget for the Santa Monica Basin has been constructed.     

Variation in microbial biomass and community structure in sediments of peter the great bay (sea of japan/east sea), as estimated from fatty acid biomarkers

Variation in the microbial biomass and community structure found in sediment of heavily polluted bays and the adjacent unpolluted areas were examined using phospholipid fatty acid analysis. Total microbial biomass and microbial community structure were responding to environmental determinants, sediment grain size, depth of sediment, and pollution due to petroleum hydrocarbons. The marker fatty acids of microeukaryotes and prokaryotes - aerobic, anaerobic, and sulfate-reducing bacteria -were detected in sediments of the areas studied. Analysis of the fatty acid profiles revealed wide variations in the community structure in sediments, depending on the extent of pollution, sediment depth, and sediment grain size. The abundance of specific bacterial fatty acids points to the dominance of prokaryotic organisms, whose composition differed among the stations. Fatty acid distributions in sediments suggest the high contribution of aerobic bacteria. Sediments of polluted sites were significantly enriched with anaerobic bacteria in comparison with clean areas. The contribution of this bacterial group increased with the depth of sediments. Anaerobic bacteria were predominantly present in muddy sediments, as evidenced from the fatty acid profiles. Relatively high concentrations of marker fatty acids of sulfate-reducing bacteria were associated with organic pollution in this site. Specific fatty acids of microeukaryotes were more abundant in surface sediments than in deeper sediment layers. Among the microeukaryotes, diatoms were an important component. Significant amounts of bacterial biomass, the predominance of bacterial biomarker fatty acids with abundance of anaerobic and sulfate-reducing bacteria are indicative of a prokaryotic consortium responsive to organic pollution.     

An improved technique for preparing eel otoliths for aging

The New Zealand Waters Pollution Regulations 1963, referring to recreational water to which the public can gain access, states that the “coliform bacteria content shall not consistently exceed 1,000/100 ml”. This standard is now under revision, and the suggested new standard is a median faecal coliform index of 200/100 ml with a maximum value not exceeding 400/100 ml.

Recent literature supports the use of faecal coliform sub‐group bacteria as the best indicator of faecal pollution and reference is made to the membership of this sub‐group. Inherent inaccuracies of the Most Probable Number (MPN) method of assessing bacterial populations are pointed out, such as experimental variations with different cultural media, and possible errors in interpretation of results. In North America, there is evidence that an MPN for the total coliform group of 1000/100 ml indicates a faecal coliform sub‐group MPN of 200/100 ml, and epidemiological experience supports these values as standards.

We tabulate and discuss evidence that the usual ratio of faecal coliforms : coliform group bacteria is typically 1 : 1 in fresh and marine waters of the Wellington region, and that a more attainable standard would be 500 faecal coliforms/100 ml. In ratios quoted in this paper, ‘coliform group’ means the remainder of the coliform group excluding faecal coliforms. The World Health Organisation (1963) definition, of the entire group of coliforms, is not intended. The ratio is different in other parts of New Zealand; in Auckland, for example, the ratio is close to that found in the United States.     

Organic biomarkers to describe the major carbon inputs and cycling of organic matter in the central Great Barrier Reef region

Controversy surrounds the sources and transport of land derived pollutants in the Great Barrier Reef ecosystem because there is insufficient knowledge of the mechanism of movement of organic contaminants and the cycling of organic matter in this dynamic system. Thus a sediment and sediment trap study was used to describe the composition of resuspended and surface sediments in the south central Great Barrier Reef and its lagoon. This region is characterised by strong tides (6–8 m at Mackay) and trade winds regularly about 15–20 knots. A series of organic biomarkers detailed the cyclical processes of sediment resuspension, recolonising with marine algae and bacteria, packaging into zooplankton faecal pellets and resettlement to sediments where the organics undergo further diagenesis. With each cycle the inshore sediments are diluted with CaCO₃ reef sediments and moved further offshore with the strong ebb tide currents. This results in transport of land derived materials offshore and little storage of organic materials in the lagoon or reef sediments. These processes were detailed by inorganic measurements such as %CaCO₃ and Al/Ca ratios, and by the compositions of hydrocarbon, sterol, alcohol, and fatty acid lipid fractions. Persistent contaminants such as coal dust from a coastal loading facility can be detected in high concentration inshore and decreasing out to the shelf break at 180 m approximately 40 nautical miles offshore. The normal processes would likely be amplified during cyclonic and other storms. The lipids show the sources of carbon to include diatoms and other phytoplankton, creanaerchaeota, sulfate reducing and other bacteria, land plants including mangrove leaves, plus coal dust and other petroleum contaminants.     

渤海西南部潮间带沉积物中的重金属

用石墨炉原子吸收分光光度法测定了渤海潮间带沉积物中Zn,Cu,Pb,Cd,Cr和Ni。研究结果表明,渤海西南部潮间带沉积物中重金属含量基本正常,但Zn的污染较为明显,可能与油田排污有关。黄河口重金属含量从高潮带向低潮带逐渐降低。本区沉积物具有相似的地球化学特性。沉积物中重金属含量与有机质含量密切相关,它们易与有机质结合,而沉降至底质。     

A multibiomarker approach in the clam Ruditapes decussatus to assess the impact of pollution in the Ria Formosa lagoon,South Coast of Portugal

The Ria Formosa lagoon is an ecosystem whose water quality reflects the anthropogenic influence upon the surrounding areas. In this lagoon, the clam Ruditapes decussatus has a great economical importance and has been widely used as a biomonitor. A multibiomarker approach (δ-aminolevulinic acid dehydratase, metallothionein, lipid peroxidation, acetylcholinesterase, alkali-labile phosphates, DNA damage) was applied to assess the environmental quality of this ecosystem and the accumulation of contaminants and their potential adverse effects on clams. Clams were sampled in different shellfish beds in the period between July 2007 and December 2008 and abiotic parameters (temperature, salinity, pH and dissolved oxygen of seawater and organic matter in the sediment), condition index, metals (Cd, Cu, Zn, Ni, Pb), TBTs and PAHs concentrations were measured in clam tissues. Data was integrated using Principal Component Analyses and biomarker indices: IBR (Integrated Biomarker Response) and HSI (Health Status Index). This multibiomarker approach enabled discrimination of a time and space trend between sites with different degrees of anthropogenic contamination, identifying one of them (site 2) as the most stressful and summer months as the most critical period for clams due to an increase of environmental stress (anthropogenic pressure along with extreme environmental conditions, e.g. temperature, dissolved oxygen, organic matter in the sediments, etc). The selected biomarkers provided an integrated response to assess the environmental quality of the system, proving to be a useful approach when complex mixtures of contaminants occur.     

Distribution and sources of surfzone bacteria at Huntington Beach before and after disinfection on an ocean outfall-- a frequency-domain analysis

Fecal indicator bacteria (FIB) were measured approximately 5 days a week in ankle-depth water at 19 surfzone stations along Huntington Beach and Newport Beach, California, from 1998 to the end of 2003. These sampling periods span the time before and after treated sewage effluent, discharged into the coastal ocean from the local outfall, was disinfected. Bacterial samples were also taken in the vicinity of the outfall during the pre- and post-disinfection periods. Our analysis of the results from both data sets suggest that land-based sources, rather than the local outfall, were the source of the FIB responsible for the frequent closures and postings of local beaches in the summers of 2001 and 2002. Because the annual cycle is the dominant frequency in the fecal and total coliform data sets at most sampling stations, we infer that sources associated with local runoff were responsible for the majority of coliform contamination along wide stretches of the beach. The dominant fortnightly cycle in enterococci at many surfzone sampling stations suggests that the source for these relatively frequent bacteria contamination events in summer is related to the wetting and draining of the land due to the large tidal excursions found during spring tides. Along the most frequently closed section of the beach at stations 3N-15N, the fortnightly cycle is dominant in all FIBs. The strikingly different spatial and spectral patterns found in coliform and in enterococci suggest the presence of different sources, at least for large sections of beach. The presence of a relatively large enterococci fortnightly cycle along the beaches near Newport Harbor indicates that contamination sources similar to those found off Huntington Beach are present, though not at high enough levels to close the Newport beaches.     

Understanding spatial and temporal dynamics of key environmental characteristics in a mesotidal Atlantic estuary (Douro,NW Portugal)

Ecosystem management and decision making process are dependent of a good knowledge of ecosystem functioning. Conceptual models allow knowledge organization through representation of relationships between variables and processes, facilitating management decisions. In this study, spatial and temporal characterization of key environmental variables, as well as relationships between them, was studied aiming the design of a conceptual model of the Douro estuary. This temperate mesotidal estuary is limited upstream by a hydroelectric power dam that controls freshwater inflow and prevents the propagation of the tide upstream, which, in turn, influences water circulation and biogeochemical dynamics of the system. During one year, from December 2002 to December 2003, water column data were collected monthly at 10 stations along the estuary, during ebb and flood tides. Spatial and temporal variability of water column salinity, temperature, nutrients, phytoplankton biomass, total particulate matter (TPM), phytoplankton primary production (PP), faecal coliform bacteria (FC) and community respiration (CR) were analysed. Salinity stratification was assessed by means of the Estuary Number (Ne) and variation of this index as well as other key characteristics with river flow was analysed. Freshwater discharge controlled salinity stratification and freshwater residence time. Ne indicated that the Douro was stratified for river flows <300 m³ s⁻¹, and freshwater residence time was >1 day for the same conditions. A decaying exponential relationship between PP and river flow was found, whereas nitrate and TPM increased logarithmically and linearly, respectively, with river flow. Regarding spatial distribution, nitrate and PP decreased downstream, showing that the river was a source of nutrients and phytoplankton, while the opposite trend was found for TPM, FC, ammonium and CR. The latter increase was probably due to untreated sewage discharge in the urbanized middle and lower estuarine stretches. Reduction of nitrate coming from the watershed and of bacterial contamination in the urban stretches of this highly modified water body, according to the European Water Framework Directive, emerges as the main water quality issues for this estuarine ecosystem.