Mediterranean Lagoon Research Articles

Heavy metals in the surface sediments of Farwa Lagoon, NW Libya: Assessment and correlation with other Mediterranean lagoons

The present study aims to evaluate the heavy metal pollution in the Farwa Lagoon, which is one of the most important coastal lagoons in NW Libya. The concentrations of six heavy metals (Fe, Zn, Pb, Ni, Cu, Cd) are measured in the surface sediment of the lagoon. Moreover, the contamination indices, including contamination factor, degree of contamination, pollution load index, geo-accumulation index, enrichment factor, risk factor, and potential ecological risk index, are applied. The results indicate that, Fe has the highest concentration, followed by Zn, Pb, Ni, Cu and Cd. The distribution patterns of metals reflect that the levels of Fe, Cu and Zn increase in the central part of the lagoon, whereas Cd and Pb increase in the central and western parts. In addition, the values of contamination factor reflect that the examined sites are moderately contaminated with Pb and Zn, whereas they are very highly contaminated with Cd. These findings lead to very high degree of contamination. Moreover, pollution load index reflects that the Farwa Lagoon is polluted. Finally, the study area is very highly ecological risk with Cd. The concentration of metals in the Farwa Lagoon is correlated with those from other regions in the Mediterranean region, such as Egypt, Algeria, Tunisia, Italy, France, and Turkey. The comparison reflects that the Farwa Lagoon has the highest concentrations of Cd and Zn.

Salinity tolerance of the invasive blue crab Callinectes sapidus: From global to local, a new tool for implementing management strategy

The latest report from the Intergovernmental Platform on Biodiversity and Ecosystem Services (IPBES) raises concerns about the global proliferation of non-native species (NIS) driven by increasing temperatures. In 2023, the invasive blue crab Callinectes sapidus experienced a significant range expansion in the French Mediterranean lagoons, now present in over 20 lagoons and numerous estuaries with different invasion gradients. It has been established that this species is eurytherm (tolerates a wide range of temperatures; 0–40 °C), rendering temperature a non-limiting factor for its proliferation. On the other hand, salinity is a critical factor to consider, as C. sapidus requires brackish water for copulation and saline water for egg maturation. In this study, we present the salinity tolerance of C. sapidus using the metabolic performance to define the tolerance of the species to a large range of salinities (13 levels from 0 to 65 psu). Results showed that C. sapidus tolerates a large range of salinities with a minimum critical threshold (CTmin) at 0 psu, an optimum at 18.5 psu, and a CTmax at 62.4 psu. Using the performance curve equation, we applied the curve to real salinity data measured each month in 2023 in 20 lagoons invaded. Using this approach, we were able to map, on a fine spatial scale, the distribution of suitable habitats for C. sapidus in the year 2023. Additionally, we have developed a tool to prioritize the lagoons based on their suitability, thereby providing a decision-making framework for management measures in each lagoon. It emerged that 50 % of lagoons were priority areas, 10 % were intermediate and 40 % required monitoring. On the basis of this approach, we can respond to European regulations to help decision-makers implement action plans and/or early detection programs for invasive species management.

Bivalve shell growth from molecular to sclerochronological scale: Environment and intrinsic factors control increment deposition

Biomineralisation of bivalve shells raises questions at the level of genes to the final calcified product. For the first time, gene expression has been studied in association with growth increment deposition in the mussel Mytilus galloprovincialis. A short-term experiment highlighted that biomineralisation genes exhibit a rhythm of expression consistent with the observed tidal increment formation. Long-term mark-recapture experiments were conducted in three Mediterranean environments and revealed that the mussel shells harbour complex incrementation regimes, consisting of daily, tidal and a mixed periodicity of ∼1.7 growth increment.d−1 formed. The latter is likely related to the local tidal regime, although the mussels were continuously submerged and exposed to a small tidal range. The pattern of growth increments shifted from mixed to daily in Mediterranean lagoon, and to tidal at sea, probably linked to biological clocks. Based on our results and the literature, a hypothetical model for mussel shell increment formation in various habitats is proposed.

Biodiversity study of the genus Bysmatrum from the South China Sea and France reveals a new benthic dinoflagellate, Bysmatrum ingrilense sp. nov. (Peridiniales, Dinophyceae)

ABSTRACT The dinoflagellate genus Bysmatrum is an unusual member of the Peridiniales and cannot be attributed to any known family. Bysmatrum differs from typical peridinialean genera in that the second and third anterior intercalary plates are separated and both antapical plates are asymmetrical. Currently, Bysmatrum encompasses six epibenthic or tide-pool species, but information on their genetic diversity and biogeography remains limited. In the present study, we obtained five strains of Bysmatrum from the South China Sea by isolating single cells and three strains from Ingril, a French Mediterranean lagoon by incubating sediments. Strains from Ingril Lagoon displayed the plate formula Po, cp, X, 4′, 3a, 7′′, 6C, 4S, 5′′′, 2′′′′. They also exhibited an elongated nucleus in the hypocone and a type B eyespot. Smooth and spherical cysts were produced in culture. Small and/or partially large subunit ribosomal DNA sequences were obtained for all eight strains. Molecular phylogeny was inferred using these concatenated sequences through maximum likelihood and Bayesian inference methods. Bysmatrum granulosum and B. subsalsum were identified from Thailand and China for the first time, each of them comprising of two ribotypes. Bysmatrum ingrilense sp. nov. was monophyletic and closest to B. subsalsum ribotype B. Pinnatoxin and related toxins were examined in two strains of Bysmatrum ingrilense by LC-MS/MS, but none were detected. Our results highlight that the diversity of Bysmatrum might be underestimated.

Validation of the Chemical and Biological Steps Required Implementing an Advanced Multi-Omics Approach for Assessing the Fate and Impact of Contaminants in Lagoon Sediments.

The increasing use of chemicals requires a better understanding of their presence and dynamics in the environment, as well as their impact on ecosystems. The aim of this study was to validate the first steps of an innovative multi-omics approach based on metabolomics and 16S metabarcoding data for analyses of the fate and impact of contaminants in Mediterranean lagoons. Semi-targeted analytical procedures for water and sediment matrices were implemented to assess chemical contamination of the lagoon: forty-six compounds were detected, 28 of which could be quantified in water (between 0.09 and 47.4 ng/L) and sediment (between 0.008 and 26.3 ng/g) samples using the UHPLC-MS/MS instrument. In addition, a non-targeted approach (UHPLC-HRMS) using four different sample preparation protocols based on solid/liquid extractions or an automated pressurized fluid extraction system (EDGE®) was carried out to determine the protocol with the best metabolome coverage, efficiency and reproducibility. Solid/liquid extraction using the solvent mixture acetonitrile/methanol (50/50) was evaluated as the best protocol. Microbial diversity in lagoon sediment was also measured after DNA extraction using five commercial extraction kits. Our study showed that the DNeasy PowerSoil Pro Qiagen kit (Promega, USA) was the most suitable for assessing microbial diversity in fresh sediment.

Strong genotype-by-environment interaction across contrasted sites for summer mortality syndrome in the Pacific oyster Crassostrea gigas

Genotype-by-environment (GxE) interaction in aquaculture is usually estimated for continuous traits and based on data from a limited number of 2–3 rearing sites. Here we report the results of a GxE study for resistance to Pacific oyster mortality syndrome (POMS), a multi-factorial disease that severely impacts Pacific oyster production worldwide. The syndrome is largely associated with Ostreid Herpes Virus 1 (OsHV-1). Resistance to OsHV-1 in Crassostrea gigas has been shown to be heritable, meaning that selective breeding is a suitable strategy for reducing mortalities. However, limited information was available about GxE interaction or the possible need to consider it in selective breeding. Survival of two cohorts (C1 and C2), consisting of a total of 104 full-sib families, was evaluated during the summer of 2013 in 7 sites along the French Atlantic, Channel and Mediterranean coasts. Mean survivals in autumn 2013 were 12.6% ± 10.9 and 4.6% ± 6.4 for C1 and C2, respectively. Genetic parameters were computed by MCMC, which is suitable for binary data like survival. Heritability estimates ranged from 0.16 to 0.42 depending on site and cohort, with a mean of 0.24 [0.20; 0.27] when including all data. GxE interactions were estimated by the genetic correlations between pairs of sites. Genetic correlations were high (ρ > 0.80) for C1 between most tidal Atlantic and Channel sites, and intermediate between tidal sites and a Mediterranean lagoon site, while they were lower and more variable for C2 (0.21–0.77). Expected genetic gains were maximal when production site was the same as selection site. They were closed to this expected maximum when the selection site was different from the production site along the Atlantic or Channel coast. Limited GxE interaction along the French Atlantic coast is favorable to wide dissemination of genetically improved oysters along this coast. Limited potential improvement was shown in the Mediterranean site if selection was carried out elsewhere, confirming the specificity of this environment. Consequently, a specific strategy such as dedicated breeding should be used to achieve genetic progress for this site.

Past and present ecological status of the soft bottom macrozoobenthos in a large mediterranean lagoon: any signals of climate change?

Coastal lagoons are transitional areas between land and sea, particularly vulnerable to human impact. The aim of this work was to compare soft bottom macrozoobenthic communities in the Lagoon of Marano and Grado, before (past period: 1993 to 1995) and after the entry into force of the Water Framework Directive-WFD (present period: 2008 to 2021). In the present period higher richness, abundances, and diversity were observed, also considering each water type (euhaline, polihaline and mesohaline) and basin (Marano and Grado) separately. The multivariate analyses also showed differences among periods and water types. According to the AMBI index, most stations were slightly disturbed in all periods and water types, and biocoenotic affinity did not vary significantly. The frequency of echinoderms increased in all water types, whereas the frequency of the polychaete Hedistediversicolor decreased in eu- and polihaline water bodies. These changes can mainly be explained by a general increase in salinity, and therefore probably the result of a marinization process, a decreasing confinement of the lagoon. As the calculation of M-AMBI is derived from AMBI, diversity and richness, this process could lead to a better ecological status sensu WFD, but with the loss of the characteristics and ecological functions of this paralic ecosystem.

Sex-Based Analysis of Length-Weight Relationships and Condition Factor in a Wild Population of Penaeus kerathurus (Decapoda: Penaeidae) from a Southwestern Mediterranean Lagoon (El Mellah Lake –Algeria)

Sex-Based Analysis of Length-Weight Relationships and Condition Factor in a Wild Population of Penaeus kerathurus (Decapoda: Penaeidae) from a Southwestern Mediterranean Lagoon (El Mellah Lake –Algeria)

Microbial Communities Associated with the Intestinal Tract of Grey Mullets from a Mediterranean Aquatic Environment

Introduction: Grey mullets comprise different species that represent the most ubiquitous teleost families in the planet’s coastal waters. They are an important proportion of the Mediterranean lagoon’s production and have been recently considered cultivated marine fish. This study aimed to explore the intestinal microbial communities of grey mullets to understand their possible ecological role for fish and the aquatic environment. Methods: Thirty-four wild-caught mullets were sampled from a Mediterranean lagoon during four seasons and the V3-V4 hypervariable regions of 16S rRNA (Illumina MiSeq) of the fish gut were sequenced. Parameters of the aquatic environment were detected: temperature, salinity, DO, PO4, NH4, NO3, NO2, SiO, DIN, and Chla. Results: The results indicated a high bacterial diversity (mean Shannon index: 4.74 ± 1.12; Simpson index: 0.93 ± 0.08) and variations among seasons. Sixty prokaryotic phyla were identified and the most abundant ones were: Proteobacteria (mean relative abundance 35.4% ± 17.9), Actinobacteriota (mean relative abundance 16.4% ± 9.9), and Firmicutes (mean relative abundance 10.1% ± 10.9). Bacteria belonging to the phylum Chloroflexi were relevant in autumn, Spirochaetota, Verrucomicrobiota, Fusobacteriota, and Cyanobacteria were particularly abundant in winter while Bacteroidota characterized summer fish. A total of 332 prokaryotic families were identified with 26 most abundant ones; Rhodociclaceae (Proteobacteria) were dominant in autumn, Brevinemataceae (Spirocheaetota) and Fusobacteriaceae (Fusobacteriota) were especially present in winter and the Staphylococcaceae (Firmicutes) prevailed in spring. Conclusion: This study sheds light on the variation in the complex gut microbial community structure of Mediterranean grey mullets and their potential ecological role in protecting fish and preserving the aquatic environment.

Environmental DNA for the surveillance of biosecurity threats in Mediterranean lagoons

Invasive species that outcompete endemic ones and toxic harmful algae that cause algal blooms threaten marine resources like fisheries, aquaculture, and even tourism. Environmental DNA (eDNA) metabarcoding can help as a method for early alert. In this study, we have analyzed communities inhabiting six lagoons within the Gulf of Lion (northwest Mediterranean Sea) with spatial protection as RAMSAR and Natura 2000 sites. Employing the COI gene as the only metabarcode, we found 15 genera that have caused recognized algal bloom outbreaks in the studied lagoons since 2000. In addition, seven alien invasive species that can pose risks to the rich marine resources of the zone and lagoons were also found. The results found from eDNA are consistent with events of toxic algae blooms before and after the sampling moment and with reported occurrences of the invasive species in nearby Mediterranean areas. Multivariate multiple analysis showed the importance of anthropic pressure in the abundance of these nuisance species. Mitigation actions and routine eDNA metabarcoding in zones of special interest like these fragile French Mediterranean lagoons are recommended for early alert of nuisance species in order to plan timely management actions.

Short-term effects of a simulated massive river flood and its recovery on sediment biogeochemistry of a Mediterranean lagoon

ABSTRACT Strong rainfalls and river floods are becoming increasingly frequent and intense in southern Europe. Mediterranean coastal lagoons, due to their hydrological characteristics, could mitigate the consequences of such events, whose effects on sediment biogeochemistry are poorly studied, yet. To provide insights on this, we investigated short-term changes in organic matter quantity, composition, nutritional quality, degradation rates, and turnover time in a lagoonal benthocosm. Both flooding and recovery phases increased the sedimentary organic load and turnover time, whereas phytopigment contents and C degradation rates were not affected. The biochemical composition varied during both phases, with an increase in carbohydrate and lipid after the flooding, and an increase in protein and chlorophyll-a after its recovery. Our results suggest that even sudden changes in salinity caused by floods and their recovery can increase sedimentary organic loads, with minor effects on their nutritional quality. The observed effects of the flooding persist in the short-term also after the recovery of the salinity, when the substrates are pre-eminently of heterotrophic origin. Our results suggest that extreme, even if short-lasting, episodic events of flooding and recovery can severely alter the benthic trophic status of coastal lagoons, having possible effects on benthic trophodynamics.

Ecological and environmental characteristics of a seagrass-dominated hypersaline coastal Mediterranean lagoon: a multidisciplinary approach

In the present paper, sedimentological, water physicochemical data and biological benthic assemblages are compiled to provide an integrated environmental assessment of a protected shallow Mediterranean lagoon with a long history of management interventions (Klisova Lagoon, Western Greece). Satellite remote sensing techniques were used for mapping the seagrass Cymodocea nodosa (Ucria) Asch, which presents an extensive expansion in the study area. The results showed that Klisova is a hypersaline, well-oxygenated lagoon presenting changes in temperature, salinity, pH and dissolved oxygen over the course of 1 year, but largely lacks any spatial differentiation other than an east–west gradient in salinity in spring and summer. Sediment was classified as silty sand to silt, rich in total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP). The benthic community was characterised by a high species richness and the presence of marine species, without a clear spatial pattern. The multivariate-AZTI’s marine biotic index (M-AMBI) showed that the ecological quality of the macrobenthos was good in most stations. C. nodosa covered over 70% of the lagoon area and formed meadows even in the eastern part of the lagoon where salinity during spring and summer was close to the reported upper tolerance limit of the species (> 50). The present multidisciplinary approach provides valuable baseline information on various components of the ecosystem which can be used as a basis for management bodies and future conservation plans for the lagoon.

An integrated trophic state assessment of a Mediterranean lagoon (Lake Manzala, Egypt) using chemical and rotifer indices

Lake eutrophication assessment is a metric that can contribute to increasing the effectiveness of future management strategies to control and reduce lake eutrophication problems. Therefore, this study aims to conduct an integrated assessment of the environmental state of Lake Manzala through chemical and biological indices of the lake eutrophication state (Trophic state index, TSI). Chemical trophic indices generally classify Lake Manzala from mesotrophic to hypertrophic. However, based on the rotifer indices results, the lake ranged between mesotrophic to eutrophic. Results indicated a significant correlation (p < 0.05) between TSI(TN), TSI(TP), TSI (chem) and TSIROT abundance, and TSIROT wet-mass. Moreover, total phosphorus (TP) and total nitrogen (TN) were the most important parameters that influenced on the rotifers, particularly in the east-south sector. The species that had the highest positive correlation with TN and TP were Brachionus quadridentatus, Philodina roseola, Brachionus calyciflorus, Lecane bulla, Keratella cochlearis, and Filinia longiseta. Based on chemical and biological indices, the water quality and ecological status of the northern and middle regions of the lake have relatively improved compared to previous periods due to the dredging and cleansing process that has been ongoing since 2017.

The Length-Weight Relationship and Condition Factors of Twelve Fish Species, with Special Reference to Cichlid species from the Mediterranean Lagoon, Lake Manzala, Egypt

The Length-Weight Relationship and Condition Factors of Twelve Fish Species, with Special Reference to Cichlid species from the Mediterranean Lagoon, Lake Manzala, Egypt

Warming and trophic structure tightly control phytoplankton bloom amplitude, composition and succession.

To better identify the responses of phytoplankton blooms to warming conditions as expected in a climate change context, an in situ mesocosm experiment was carried out in a coastal Mediterranean lagoon (Thau Lagoon, South of France) in April 2018. Our objective was to assess both the direct and indirect effects of warming on phytoplankton, particularly those mediated by top-down control. Four treatments were applied: 1) natural planktonic community with ambient water temperature (C); 2) natural planktonic community at +3°C elevated temperature (T); 3) exclusion of larger zooplankton (> 200 μm; mesozooplankton) leaving microzooplankton predominant with ambient water temperature (MicroZ); and 4) exclusion of larger zooplankton (> 200 μm; mesozooplankton) at +3°C elevated temperature (TMicroZ). Warming strongly depressed the amplitude of the phytoplankton bloom as the chlorophyll a concentration was twice lower in the T treatment. This decline under warmer conditions was most likely imputed to increase top-down control by zooplankton. However, removal of mesozooplankton resulted in an opposite trend, with a higher bloom amplitude observed under warmer conditions (MicroZ vs. TMicroZ) pointing at a strong interplay between micro- and mesozooplankton and the effect of warming for the spring phytoplankton blooms. Furthermore, both warming and mesozooplankton exclusion induced shifts in phytoplankton community composition during bloom and post-bloom periods, favoring dinoflagellates and small green algae at the expense of diatoms and prymnesiophytes. Moreover, warming altered phytoplankton succession by promoting an early bloom of small green flagellates, and a late bloom of diatoms. Our findings clearly highlighted the sensitivity of phytoplankton blooms amplitudes, community composition and succession patterns to temperature increases, as well as the key role of initial zooplankton community composition to elicit opposite response in bloom dynamics. It also points out that warmer conditions might favor dinoflagellates and small green algae, irrespective of zooplankton community composition, with potential implications for food web dynamics and energy transfer efficiency under future ocean condition.

Toward coherent space–time mapping of seagrass cover from satellite data: an example of a Mediterranean lagoon

Abstract. Seagrass meadows are a highly productive and economically important shallow coastal habitat. Their sensitivity to natural and anthropogenic disturbances, combined with their importance for local biodiversity, carbon stocks, and sediment dynamics, motivate a frequent monitoring of their distribution. However, generating time series of seagrass cover from field observations is costly, and mapping methods based on remote sensing require restrictive conditions on seabed visibility, limiting the frequency of observations. In this contribution, we examine the effect of accounting for environmental factors, such as the bathymetry and median grain size (D50) of the substrate as well as the coordinates of known seagrass patches, on the performance of a random forest (RF) classifier used to determine seagrass cover. Using 148 Landsat images of the Venice Lagoon (Italy) between 1999 and 2020, we trained an RF classifier with only spectral features from Landsat images and seagrass surveys from 2002 and 2017. Then, by adding the features above and applying a time-based correction to predictions, we created multiple RF models with different feature combinations. We tested the quality of the resulting seagrass cover predictions from each model against field surveys, showing that bathymetry, D50, and coordinates of known patches exert an influence that is dependent on the training Landsat image and seagrass survey chosen. In models trained on a survey from 2017, where using only spectral features causes predictions to overestimate seagrass surface area, no significant change in model performance was observed. Conversely, in models trained on a survey from 2002, the addition of the out-of-image features and particularly coordinates of known vegetated patches greatly improves the predictive capacity of the model, while still allowing the detection of seagrass beds absent in the reference field survey. Applying a time-based correction eliminates small temporal variations in predictions, improving predictions that performed well before correction. We conclude that accounting for the coordinates of known seagrass patches, together with applying a time-based correction, has the most potential to produce reliable frequent predictions of seagrass cover. While this case study alone is insufficient to explain how geographic location information influences the classification process, we suggest that it is linked to the inherent spatial auto-correlation of seagrass meadow distribution. In the interest of improving remote-sensing classification and particularly to develop our capacity to map vegetation across time, we identify this phenomenon as warranting further research.

Tracing Groundwater Sources in Coastal Food Webs: Nitrogen and Carbon Isotope Values in Mussels in a Mediterranean Lagoon

Tracing Groundwater Sources in Coastal Food Webs: Nitrogen and Carbon Isotope Values in Mussels in a Mediterranean Lagoon

Modelling spatiotemporal distributions of Vulcanodinium rugosum and pinnatoxin G in French Mediterranean lagoons: Application to human health risk characterisation

Consumption of seafood contaminated by phycotoxins produced by harmful algae is a major issue in human public health. Harmful algal blooms are driven by a multitude of environmental variables; therefore predicting human dietary exposure to phycotoxins based on these variables is a promising approach in health risk management. In this study, we attempted to predict the human health risks associated with Vulcanodinium rugosum and its neurotoxins, pinnatoxins (PnTXs), which have been regularly found in Mediterranean lagoons since their identification in 2011. Based on environmental variables collected over 1 year in four Mediterranean lagoons, we developed linear mixed models to predict the presence of V. rugosum and PnTX G contamination of mussels. We found that the occurrence of V. rugosum was significantly associated with seawater temperature. PnTX G contamination of mussels was highest in summer but persisted throughout the year. This contamination was significantly associated with seawater temperature and the presence of V. rugosum with a time lag, but not with dissolved PnTX G in seawater. By using the contamination model predictions and their potential variability/uncertainty, we calculated the human acute dietary exposures throughout the year and predicted that 25% of people who consume mussels could exceed the provisional acute benchmark value during the warmest periods. We suggest specific recommendations to monitor V. rugosum and PnTX G.

Comparative evaluation of Ostrea edulis (Linnaeus, 1758) and Crassostrea gigas (Thunberg, 1793) biodeposition in Mediterranean lagoons and under controlled conditions

Oyster farming is considered a sustainable seafood production with environmental benefits related to water purification, but negative effects on the benthic ecosystem functioning could be caused by the release of feaces and pseudofeaces, collectively called bio-deposits. In this study, we compared the first time the daily bio-deposit production of Crassostrea gigas and Ostrea edulis in two Mediterranean coastal lagoons and in laboratory-controlled conditions. C. gigas resulted in a higher bio-deposit production than O. edulis in all the treatments, due to a higher ingestion rate of the former. Regardless to the species, differences were also recorded between lagoons, resulting S’Ena Arrubia in a higher bio-deposit production, consistent with a higher quality (i.e. POM/TPM ratio) and sedimentation rate of seston, than Corru S’Ittiri, indicating that the bio-deposition is strongly related to the environmental and trophic conditions of the farming site. Our results suggest that the bio-deposit production is site-specific, and it must be evaluated specifically in each farming site and for each oyster species. This study presents new data on the bio-deposition of C. gigas and O. edulis and contributes to our understanding of the potential impact of oyster farming.

Response of Phytoplankton Communities to Variation in Salinity in a Small Mediterranean Coastal Lagoon: Future Management and Foreseen Climate Change Consequences

Mediterranean coastal lagoons are particularly vulnerable to increasing direct anthropogenic threats and climate change. Understanding their potential responses to global and local changes is essential to develop management strategies adapted to these ecosystems. Salinity is a fundamental structuring factor for phytoplankton communities; however, its role under climate change is understudied. We hypothesized that salinity variations imposed by climate change and/or management actions could disturb Mediterranean lagoons’ phytoplankton communities. To test our hypothesis, we performed two 5-day microcosm experiments in which natural phytoplankton assemblages from the Santa Giulia lagoon (Corsica Island) were subjected to three increasing (53–63–73) and decreasing (33–26–20) levels of salinity, to mimic strong evaporation and flash flooding, respectively. Results indicate that over-salinization inhibited growth and modified the assemblages’ composition. Freshening, on the contrary, showed feeble effects, mainly boosting microphytoplankton abundance and depleting diversity at lowest salinity. In both experiments and under freshening in particular, initially rare species emerged, while photosynthetic activity was degraded by salinity increase only. We demonstrated that phytoplankton communities’ structure and metabolism are strongly altered by the predicted implications of climate change. Such impacts have to be considered for future management of coastal lagoons (control of sea exchanges and watershed fluxes). This work constitutes a priority step towards the proactive adapted management and conservation of such as-yet-neglected ecosystems in the context of climate change.