Plankton Biomass Research Articles

ENSO-induced co-variability of Salinity, Plankton Biomass and Coastal Currents in the Northern Gulf of Mexico

The northern Gulf of Mexico (GoM) is a region strongly influenced by river discharges of freshwater and nutrients, which promote a highly productive coastal ecosystem that host commercially valuable marine species. A variety of climate and weather processes could potentially influence the river discharges into the northern GoM. However, their impacts on the coastal ecosystem remain poorly described. By using a regional ocean-biogeochemical model, complemented with satellite and in situ observations, here we show that El Niño - Southern Oscillation (ENSO) is a main driver of the interannual variability in salinity and plankton biomass during winter and spring. Composite analysis of salinity and plankton biomass anomalies shows a strong asymmetry between El Niño and La Niña impacts, with much larger amplitude and broader areas affected during El Niño conditions. Further analysis of the model simulation reveals significant coastal circulation anomalies driven by changes in salinity and winds. The coastal circulation anomalies in turn largely determine the spatial extent and distribution of the ENSO-induced plankton biomass variability. These findings highlight that ENSO-induced changes in salinity, plankton biomass, and coastal circulation across the northern GoM are closely interlinked and may significantly impact the abundance and distribution of fish and invertebrates.

High Frequency Multi-Year Variability in Baltic Sea Microbial Plankton Stocks and Activities.

Marine bacterioplankton are essential in global nutrient cycling and organic matter turnover. Time-series analyses, often at monthly sampling frequencies, have established the paramount role of abiotic and biotic variables in structuring bacterioplankton communities and productivities. However, fine-scale seasonal microbial activities, and underlying biological principles, are not fully understood. We report results from four consecutive years of high-frequency time-series sampling in the Baltic Proper. Pronounced temporal dynamics in most investigated microbial variables were observed, including bacterial heterotrophic production, plankton biomass, extracellular enzyme activities, substrate uptake rate constants of glucose, pyruvate, acetate, amino acids, and leucine, as well as nutrient limitation bioassays. Spring blooms consisting of diatoms and dinoflagellates were followed by elevated bacterial heterotrophic production and abundances. During summer, bacterial productivity estimates increased even further, coinciding with an initial cyanobacterial bloom in early July. However, bacterial abundances only increased following a second cyanobacterial bloom, peaking in August. Uptake rate constants for the different measured carbon compounds varied seasonally and inter-annually and were highly correlated to bacterial productivity estimates, temperature, and cyanobacterial abundances. Further, we detected nutrient limitation in response to environmental conditions in a multitude of microbial variables, such as elevated productivities in nutrient bioassays, changes in enzymatic activities, or substrate preferences. Variations among biotic variables often occurred on time scales of days to a few weeks, yet often spanning several sampling occasions. Such dynamics might not have been captured by sampling at monthly intervals, as compared to more predictable transitions in abiotic variables such as temperature or nutrient concentrations. Our study indicates that high resolution analyses of microbial biomass and productivity parameters can help out in the development of biogeochemical and food web models disentangling the microbial black box.

Biomass of plankton and macrobenthos and benthic species diversity in relation to environmental gradients in a nationwide coastal survey

Using Korean coastal survey data, we examined the relationships between plankton and benthic biomass and environmental parameters. The nitrate in coastal waters was mainly derived from the influx of fresh water, whereas much of the ammonium originated from decomposing organic matter in the sediments and river discharge. Phytoplankton and zooplankton concentrations were positively related to the amount of suspended particulate matter (SPM), but decline when SPM becomes high (> 10 ppm). Particulate organic carbon (POC) comprised about 40% of the SPM, suggesting that organic matters associated with river-borne sediments and re-suspended particles are a large source of coastal water POC. Zooplankton abundance was more closely related to the distribution of phytoplankton than to that of POC. Benthic biomass showed a dome-shaped relationship with the water column POC concentration, but no clear relationship with sediment POC distribution. The biodiversity of macrobenthic animals gradually decreases when POC exceeds 1% of the sediment weight. Reduction of siltation and POC could lead to enhanced benthic–pelagic coupling via increased plankton biomass and productivity, as well as overall increased benthic diversity in coastal environments.

River habitat homogenisation enhances trophic competition and promotes individual specialisation among young of the year fish

Abstract In large rivers, fish ontogenic development success is mainly influenced by resource availability and by the possibility of species to adapt their diet (i.e. trophic niche). Humans have drastically modified freshwater habitats, notably for navigation purposes. Such modifications may reduce food availability for young of the year (YOY) fish and, consequently, influence their ability to reach the adult age. In the Meuse River, decrease of fish abundance is thought to be linked to a drastic reduction of phytoplankton biomass. In this context of decreasing phytoplankton biomass, we studied trophic niches of three cyprinid species (common bleak Alburnus alburnus, chub Squalius cephalus, and roach Rutilus rutilus) and one percid species (European perch Perca fluviatilis) at various stages of development, using stable isotope analysis in order to compare intra‐ and interspecific competition between sites differing in degree of channelisation. Two reaches of the Meuse River differing by their degree of regulation were investigated. We hypothesised that habitat homogenisation would (1) decrease food resource availability and diversity and (2) increase trophic competition, particularly among earlier ontogenic stages, and promote individual specialisation. Our study provides evidence that in the context of low planktonic biomass, most YOY relied on benthic food sources. Furthermore, the Meuse River flow and depth regulation significantly impacted the abundance and species richness of YOY. In the heavily channelised reach, between‐stages competition and low resource diversity lead to an increase in diet partitioning between cyprinid larvae, as well as consumption of non‐optimal energetic food sources such as aquatic vegetation by some individuals. By contrast, in the less channelised reach, larvae displayed a generalist feeding habit focusing on high energy content prey such as different taxa of macroinvertebrates, suggesting that the diversity of habitat reduces the food competition within and between stages. Intraspecific resource repartition is a key point for YOY fish having to cope with plankton‐depleted conditions. Younger cyprinid stages seem more affected by intra‐ and inter‐specific competition in the more channelised reach. YOY fish communities were also less diversified and abundant in the more altered site, which highlight the importance of limiting channelisation to better conserve fish communities.

ОРГАНИЧЕСКОЕ ВЕЩЕСТВО ДОННЫХ ОСАДКОВ ЗОНЫ ГИДРОТЕРМАЛЬНОЙ АКТИВНОСТИ (РАЙОН БУХТЫ ФРОЛИХА, СЕВЕРНЫЙ БАЙКАЛ)

The organic matter of bottom sediments enriched by biomass of plankton or pine needles has been studied with a complex of geochemical methods (pyrolysis, bituminological and biomarker analyses). The maturity of the organic matter remains low (PK1) even after thermobaric cultivation (in conditions of protokatageneza at temperature of +80°С and pressure of 25 bar).

Plankton community interactions in an Amazonian floodplain lake, from bacteria to zooplankton

The simple view of the classical phytoplankton–zooplankton–fish food chain (CFC) has been replaced by a more complex framework, integrating microbial compartments (microbial food web, MFW). Few studies considered all components of the pelagic MFW in freshwaters and mostly are from temperate regions. We investigated carbon partitioning in the CFC and the MFW in an Amazonian floodplain system and analyzed the strength of interactions among components through structure equation modeling. We hypothesized that (i) MFW contributes highly to total plankton biomass throughout the year; and (ii) all plankton communities increase in biomass during low water, increasing the role of trophic interactions. We collected 30 subsurface samples (nutrients and plankton communities). MFW predominated over CFC in carbon biomass, and plankton components and their interactions changed according to the contrasting water level. Because phosphorus can be a potentially limiting resource for strict primary producers, higher biomass and a more complex MFW occurred during low water. We concluded that hydrology is a key factor shaping biotic interactions during low-water periods, and that MFW plays a key role in floodplain lakes, being potential mixotrophy an important strategy for phytoplankton.

Flow Regime and Nutrient-Loading Trends from the Largest South European Watersheds: Implications for the Productivity of Mediterranean and Black Sea’s Coastal Areas

In the last century, large watersheds in Southern Europe have been impacted by a combination of anthropogenic and climatic pressures, which have rapidly evolved to change the ecological status of freshwater and coastal systems. A comparative analysis was performed for Ebro, Rhône, Po and Danube rivers, to investigate if they exhibited differential dynamics in hydrology and water quality that can be linked to specific human and natural forces acting at sub-continental scales. Flow regime series were analyzed from daily to multi-decadal scales, considering frequency distributions, trends (Mann–Kendall and Sen tests) and discontinuities (SRSD Method). River loads of suspended matter, nutrients and organic matter and the eutrophication potential of river nutrients were estimated to assess the impact of river loads on adjacent coastal areas. The decline of freshwater resources largely impacted the Ebro watershed on annual (−0.139 km3 yr−1) and seasonal (−0.4% yr−1) scales. In the other rivers, only spring–summer showed significant decreases of the runoff coupled to an exacerbated flow variability (0.1–0.3% yr−1), which suggested the presence of an enhanced regional climatic instability. Discontinuities in annual runoff series (every 20–30 years) indicated a similar long-term evolution of Rhône and Po rivers, differently from Ebro and Danube. Higher nutrient concentrations in the Ebro and Po (+50%) compared to Rhône and Danube and distinct stoichiometric nutrient ratios may exert specific impacts on the growth of plankton biomass in coastal areas. The overall decline of inorganic phosphorus in the Rhône and Po (since the 1980s) and the Ebro and Danube (since the 1990s) mitigated the eutrophication in coastal ecosystems inducing, however, a phase in which the role of organic phosphorus loads (Po > Danube > Rhône > Ebro) on coastal productivity could be more relevant. Overall, the study showed that the largest South European watersheds are differently impacted by anthropogenic and climatic forces and that this will influence their vulnerability to future changes of flow regime and water quality.

Treatment of real flue gas desulfurization wastewater in an autotrophic biocathode in view of elemental sulfur recovery: Microbial communities involved

Sulfur oxide emissions can lead to acidic precipitation and health concerns. Flue gas desulfurization (FGD) systems treat these emissions generating a wastewater with high-sulfate content. This work is the first attempt to treat this effluent with bioelectrochemical systems (BES) in order to recover elemental sulfur, a technology that allows the treatment of several wastewaters that lack of electron donor. The sulfate treatment and elemental sulfur recovery have been studied in a biocathode with simultaneous sulfate reduction to sulfide and partial sulfide oxidation, comparing the performance obtained with synthetic and real wastewater. A decrease of the sulfate removal rate (SRR) from 108 to 73mgS-SO42−L−1d−1 was observed coupled to an increase in the elemental sulfur recovery from 1.4 to 27mgS-S0L−1d−1. This elemental sulfur recovered as a solid from the real wastewater represented a 64% of the theoretical elemental sulfur produced (the elemental sulfur corresponded to a 72% of the solid weight). In addition, microbial communities analysis of the membrane and cathode biofilms and planktonic biomass showed that the real wastewater allowed a higher growth of sulfur oxidizing bacteria (SOB) adapted to more complex waters as Halothiobacillus sp. while decreasing the relative abundance of sulfate reducing bacteria (SRB).

A model for monitoring the evolution of the Black Sea ecosystem on the basis of remote sensing data assimilation

ABSTRACTThe study presents some results of the Black Sea ecosystem dynamics during about twenty years (1998–2016), based on numerical simulations with the assimilation of remote-sensing data. The 3D model of the lower trophic level marine ecosystem is a one-way, off-line coupled with circulation model. It describes processes in the layer from the sea surface to 200 m depth and includes 15 state variables. The ecosystem model assimilates the satellite measurements which are the maps of the surface chlorophyll concentration fields reconstructed based on the remote-sensing data from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS, satellite OrbView) and Moderate Resolution Imaging Spectroradiometer (MODIS, satellites Aqua and Terra) using the regional optical model of the Black Sea. The assimilation technique is based on optimal interpolation and nudging procedure. The results of the simulation were validated using the Black Sea Oceanographic Database, which contains the direct measurements of chlorophyll, nitrates, and dissolved oxygen concentrations in seawater. Comparison of the simulation data with measurements showed that the simulated fields satisfactorily reproduce seasonal variability and vertical distribution. In addition to in situ measurements, the obtained surface chlorophyll distributions were also compared with the satellite data. The simulation results allowed analysing the inter-annual and seasonal variability of the main parameters of the Black Sea pelagic ecosystem. Evolution of the plankton biomass in the upper 50 m layer shows a negative linear trend, which is followed by reduction of the nitrates content in this layer.

Variation in the plankton abundance, biomass and diversity of Municipal pond and Bukvora Baor at Jashore district, Bangladesh

Variation in the plankton abundance, biomass and diversity of Municipal pond and Bukvora Baor at Jashore district, Bangladesh

Machine learning predictions of trophic status indicators and plankton dynamic in coastal lagoons

Multivariate trophic indices provide an efficient way to assess and classify the eutrophication level and ecological status of a given water body, but their computation requires the availability of experimental information on many parameters, including biological data, that might not always be available. Here we show that machine learning techniques – once trained against a full data set – can be used to infer plankton biomass information from chemical and physical parameter only, so that trophic index can then be computed without using additional biological data. More specifically, we reconstruct plankton information from chemical and physical data, and this information together with chemical data was used to compute the TRIX, which was eventually used to assess the eutrophication status of the water body. The RF was also used to evaluate the prevailing mechanism (bottom-up versus top-down) controlling plankton dynamic. The case study was a Mediterranean lagoon, the Ghar El Melh Lagoon, which has been used as a natural laboratory to test the effectiveness of the proposed approach. Based on the resulting TRIX values (4.2 in April – 5.7 in December) the Ghar El Melh Lagoon can be classified an eutrophic ecosystem. This modeling process suggests that phytoplankton growth in Ghar El Melh Lagoon is mainly bottom-up control by nutrients availability, whereas the top-down control exerted by the zooplankton is relatively weak. Results highlight that in bottom up controlled lagoon machine learning technique can efficiently be used to compute ecological indicators even with low availability of biological data.

Evaluation of Mixotrophy-Associated Gene Expression in Two Species of Polar Marine Algae

Mixotrophic flagellates can comprise significant proportions of plankton biomass in marine ecosystems. Despite the growing recognition of the importance of this ecological strategy, and the identification of major environmental factors controlling phagotrophic behavior (light and nutrients), the physiological and molecular mechanisms underlying mixotrophic behavior are still unclear. In this study, we performed RNA-Seq transcriptomic analysis for two mixotrophic prasinophytes, Micromonas polaris and Pyramimonas tychotreta, under dissolved nutrient regimes that altered their ingestion of bacteria prey. Though the strains examined were polar isolates, both belong to genera with widespread distribution. Our aim was to characterize the transcriptomes of these two non-model phytoflagellates, identify transcripts consistent with phagotrophic activity and assess their differential expression in response to nutrient stress. De novo assembly of the transcriptomes yielded large numbers of novel coding transcripts with no known match within public databases. A summary of the transcripts by Gene Ontology terms showed many expected expression patterns, including genes involved in photosynthetic pathways and enzymes implicated in nutrient uptake pathways. Searches of KEGG databases identified several genes associated with intra-cellular digestive pathways actively transcribed in both prasinophytes. Differential expression analysis showed a larger response in P. tychotreta, where 23,373 genes were up-regulated and 1,752 were down-regulated in the low nutrient treatment when phagotrophy was enhanced. In contrast, in M. polaris, low nutrient treatments resulted in up-regulation of 314 transcripts while down-regulating 371. With respect to phagotrophic-related expression, 37 genes were co-expressed in both P. tychotreta and M. polaris, and although the response was less pronounced in M. polaris, it is consistent with differences in observed ingestion behavior. This study presents the first genomic data for Pyramimonas tychotreta, and also contributes to the limited available data for Micromonas polaris. Furthermore, it provides insight into the presence of genes associated with phagocytosis within the Prasinophyceae and contributes to the understanding of potential target genes required for the construction of a complete model of gene regulation of phagocytic behavior in algae.

Structure of the Biotic Component in the Rybinsk Reservoir Ecosystem: Importance of Heterotrophic Bacteria (Review)

The total biomass of the biotic component of the ecosystem has been determined and the contribution of the main ecological groups—autotrophic and heterotrophic organisms from different habitats—to its formation has been estimated in a large plain meso-eutrophic reservoir (Rybinsk Reservoir, Upper Volga). Particular attention is paid to the role of heterotrophic bacteria in the structure and functioning of the biota in the reservoir. The total biomass of the biotic component of the ecosystem is 71536 t C, which is 5.2% of the total organic carbon in the reservoir. Higher aquatic plants make the largest contribution to the formation of the biomass in the reservoir. Their biomass, including epiphyton, was 6.0 and 1.9 times larger than the biomass of plankton and benthos, respectively. Heterotrophic bacteria, most of which inhabit bottom sediments, rank second in respect to their contribution to the total biomass. The comparison of the total primary production of all phototrophic organisms and the carbon demand of heterotrophic bacteria indicates the importance of allochthonous organic matter in the functioning of the reservoir ecosystem.

A tale of two eras: Phytoplankton composition influenced by oceanic paleochemistry.

We report the results of simple experiments which support the hypothesis that changes in ocean chemistry beginning in the Mesozoic Era resulted in an increase in the nutritional quality per mole of C and per cell of planktonic algal biomass compared to earlier phytoplankton. We cultured a cyanobacterium, a diatom, a dinoflagellate, and a green alga in media mimicking aspects of the chemistry of Palaeozoic and Mesozoic-Cenozoic oceans. Substantial differences emerged in the quality of algal biomass between the Palaeozoic and Mesozoic-Cenozoic growth regimes; these differences were strongly affected by interspecific interactions (i.e., the co-existence of different species alters responses to the chemistry of the medium). The change was in the direction of a Mesozoic-Cenozoic biomass enriched in protein per mole C, although cells contained less carbon overall. This would lead to a lower C:N ratio. On the assumption that Mesozoic-Cenozoic grazers' assimilation of total C was similar to that of their earlier counterparts, their diet would be stoichiometrically closer to their C:N requirement. This, along with an increase in mean cell size among continental shelf phytoplankton, could have helped to facilitate observed evolutionary changes in the Mesozoic marine fauna. In turn, increased grazing pressure would have operated as a selective force for the radiation of phytoplankton clades better equipped with antigrazing capabilities (sensu lato), as found widely in phytoplankton with biomineralization. Our results emphasize potential links between changing seawater chemistry, increased predation pressure and the rise to ecological dominance of chlorophyll a+c algae in Mesozoic oceans. The experiments also suggest a potential role for ocean chemistry in changes of marine trophic structure from the Palaeozoic to the later Mesozoic Era.

Effects of flask configuration on biofilm growth and metabolites of intertidal Cyanobacteria isolated from a mangrove forest.

A novel approach was employed to study the growth of three cyanobacterial strains namely Oscillatoria sp. (AP17), Leptolyngbya sp. (AP3b) and Chroococcus sp. (AP3U). Furthermore, their broad metabolite profile, production of pigments, exopolysaccharide (EPS) and antimicrobial activity were evaluated in response to contrasting cultivation modes: biofilm or planktonic. The biofilm culture mode was carried out in the patented conico-cylindrical flask (CCF) and the planktonic culture mode was carried out in an Erlenmeyer flask (EF). The amount of polysaccharide that was released and that remained capsular/bound was higher in CCF compared to EF cultivation. Amount of chlorophyll a produced by Oscillatoria (AP17) was higher in the CCF compared to the EF cultivation. Highest antimicrobial activities were exhibited by Leptolyngbya (AP3b) biofilm than other biofilms as well as planktonic biomass. Metabolite profiles of Cyanobacteria were revealed by various chromatographic techniques and showed clear differences among the two contrasting modes of cultivation. The results showed clear differences in the mode of growth for achieving maximum chlorophyll a, EPS and bioactive metabolite production of the Cyanobacteria. The present study augmented the information which can enhance wider exploration of the biofilm mode of cultivation of Cyanobacteria.

Mathematical Modeling of Plankton Biomass Dynamics During the Spring Thermal Bar in Kamloops Lake

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Differences in planktonic ciliate spatial distribution in spring and autumn in the southern Yellow Sea

Seasonal variation of marine plankton spatial distribution is important in understanding the biological processes in the ocean. In this study, we studied spatial distribution of planktonic ciliate abundance and biomass in the central deep area (station depth greater than 60 m) and the coastal shallow area (station depth less than 60 m) of the southern Yellow Sea (32°–36.5°N, 121°–125°E) in spring (April) and autumn (October–November) of 2006. Our results showed that both ciliate abundance and biomass in the surface waters were higher in spring ((1 490±2 336) ind./L; (4.11±7.81) μg/L) than in autumn ((972±823) ind./L; (1.11±1.18) μg/L, calculated by carbon). Ciliate abundance and biomass in the surface waters of the coastal shallow area were similar in spring and autumn. However, in the central deep area, those values were much higher in spring ((1 878±2 893) ind./L; (5.99±10.10) μg/L) than in autumn ((738±373) ind./L; (0.74±0.76) μg/L). High values of ciliate abundance and biomass occurred in the central deep area in spring and in the coastal shallow area in autumn. Mixotrophic ciliate Laboea strobila was abundant in the central deep area in spring, when a phytoplankton bloom occurred. However, in autumn, L. strobila was abundant in the coastal shallow area. Boreal tintinnid Ptychocyli obtusa was found in spring. Both L. strobila and P. obtusa were concentrated in the surface waters when their abundance was more than 1 000 ind./L. Peaks of these species were in the subsurface waters when their abundance was less than 400 ind./L. This study showed that both high abundance and biomass of ciliates occurred in different areas in southern Yellow Sea seasonally.

PRESENT STATE OF THE SPRING PLANKTON COMMUNITY IN THE NORTHERN OKHOTSK SEA (1997–2017)

Two periods are clearly distinguished within the last two decades (1997–2017) by several quantitative parameters of the plankton community in the northern shelf zone of the Okhotsk Sea: the period of high productivity in the 1997–2005 with the biomass of 1000–1200 mg/m3 and the period of medium productivity in the 2006–2017 with the biomass of 550–580 mg/m3. The sharp drop of the biomass had occurred in just one year because of decreasing of the large-sized zooplankton abundance (euphausiids, mysids, hyperiids, and pteropods) that formed the bulk of the food base for commercial species of nekton. After the drop, the plankton biomass had stabilized again. The similar decreasing was observed earlier, in 1998, as the result of several warm years, but in those times the zooplankton abundance restored its maximal values in 2 years. Correlations of the large-sized zooplankton dynamics with the thermal parameters, as the cold subsurface layer temperature and the maximum and mean values of the ice cover are considered. Generally, the period of high productivity was distinguished by cold environments, and they were warmer in the period of medium productivity.

Effects of the Nile tilapia (Oreochromis niloticus L.) on the plankton community of a tropical reservoir during and after an algal bloom

The invasive species Nile tilapia is a filter-feeding omnivorous fish that can have a negative effect on zooplankton and phytoplankton resources. However, the strength of its effects on plankton communities should decrease with increasing plankton biomass, e.g., during an algal bloom. We tested this hypothesis by performing two experiments in a tropical reservoir, where we randomly allocated two treatments (with and without tilapia) to 20 mesocosms. The first experiment was conducted during an algal bloom (biovolume = 1038.34 mm3 l−1), while the second experiment was conducted after the bloom (biovolume = 1.05 mm3 l−1). The negative effects of fish on mesozooplankton (mean size of 480 µm in both experiments) and large algae (GALD ≥ 50 µm) were stronger in the second than in the first experiment. On the other hand, the negative effects of fish on microzooplankton (experiment 1: mean size 180 µm; experiment 2: mean size 128 µm) and small algae (GALD < 50 µm) were stronger in the first than in the second experiment. We conclude that the Nile tilapia can suppress phytoplankton and zooplankton biomass in tropical lakes and reservoirs, but the magnitude of this effect depends on plankton biomass and size-structure.

San Francisco Bay nutrients and plankton dynamics as simulated by a coupled hydrodynamic-ecosystem model

An open source coupled physical-biogeochemical model is developed for San Francisco Bay (SFB) to study nutrient cycling and plankton dynamics as well as to assist ecosystem based management and risk assessment. The biogeochemical model in this study is based on the Carbon, Silicate and Nitrogen Ecosystem (CoSiNE) model, and coupled to the unstructured grid, Semi-Implicit Cross-scale Hydroscience Integrated System Model (SCHISM). The SCHISM-CoSiNE model reproduces the spatial and temporal variability in nutrients and plankton biomass, and its physical and biogeochemical performance is successfully tested using comparisons with shipboard and fixed station observations. The biogeochemical characteristics of the SFB during wet and dry years are investigated by changing the input of the major rivers. River discharges from the Sacramento and San Joaquin Rivers affect the phytoplankton biomass in North SFB through both advection and dilution of nutrient (including ammonium, NH4) concentrations in the river. The reduction in residence time caused by increased inflows can result in decreased biomass accumulation, while the corresponding reduction in NH4 concentration favors the growth of biomass. In addition, the model is used to make a series of sensitivity experiments to examine the response of SFB to changes in 1) nutrient loading from rivers and wastewater treatment plants (WWTPs), 2) a parameter (ψ) defining NH4 inhibition of nitrate (NO3) uptake by phytoplankton, 3) bottom grazing and 4) suspended sediment concentration. The model results show that changes in NH4 input from rivers or WWTPs affect the likelihood of phytoplankton blooms via NH4 inhibition and that the choice of ψ is critical. Bottom grazing simulated here as increased plankton mortality demonstrates the potential for bivalve reduction of chlorophyll biomass and the need to include bivalve grazing in future models. Furthermore, the model demonstrates the need to include sediments and their contribution to turbidity and availability of light. This biogeochemical model is suitable for other estuaries with similar ecological issues and anthropogenic stressors.