Jesús M. Mercado

Satellite monthly time series of temperature, salinity, and chlorophyll a (Chl a) for the period 2016–2025 were analyzed to assess the importance of river discharges in shaping productivity patterns in the marine area of Guinea‐Bissau (11–12°N), one of the most productive ecosystems in the world. Chl a exhibited a annual cycle, with maxima in April-June and minima in August, consistent with that described for the Canary Current Large Marine Ecosystem, where annual maxima are primarily driven by wind‐induced coastal upwelling along the Mauritania-Senegal margin. However, in our dataset, the reduction in Chl a during the low‐productivity period was much less pronounced at stations located near the coast (7.6 µg L⁻¹ compared with 4.2 µg L⁻¹). Moreover, a second, less intense seasonal maximum appeared in November, coinciding with the lowest salinity values. The intensity of the spring maximum decreased toward the coast, whereas the autumn maximum increased near the coast. On an annual basis, coastal Chl a was approximately 20% higher than offshore values, and this difference increased to about 60% from June to December. This pattern suggests that the autumn peak is not driven by oceanic dynamics but is instead linked to river discharges, consistent with the tropical hydroclimatic forcing characteristic of the Guinea Current Large Marine Ecosystem. Increasing trends in temperature and salinity from 2016 to 2024, along with a negative Chl a trend at offshore stations were also btained likely related to variability in global ocean circulation associated with ENSO and La Niña, which reduces upwelling intensity. However, no negative Chl a trend was detected at coastal stations, likely because productivity there is sustained by riverine inputs supporting the importance of terrestrial nutrient inputs in sustaining primary production.

Background: Coastal ecosystems face increasing threats from eutrophication, driven by excess nutrient inputs that lead to ecosystem-disruptive algal blooms (EDABs). The Mar Menor coastal lagoon, located in the south-eastern Iberian Peninsula, has experienced severe ecological disruption since 2015, beginning with a Synechococcus ‑dominated cyanobacterial bloom and followed by major shifts in eukaryotic phytoplankton composition. However, the mechanisms that affect phytoplankton dynamics in this coastal environment remain unknown. Here, we investigate the spatiotemporal dynamics of prokaryotic communities in the lagoon after the initial Synechococcus bloom using three years of 16S rRNA gene sequencing data and evaluate how environmental factors shape these patterns. In addition, we examine the fine‑scale diversity and dynamics of Synechococcus variants through metagenomics ( petB gene) and use genome‑resolved analyses to identify functional traits associated with their succession in the lagoon. Finally, to investigate the role of biotic interactions in regulating cyanobacterial growth, we examine the temporal dynamics of cyanophages. Results: Microbial communities in the waters of the Mar Menor responded rapidly and consistently to short‑term environmental fluctuations and showed a weak seasonal signal in alpha and beta diversity. Prokaryotic assemblages associated with two deoxygenation events following extreme weather conditions (intense rainfall in autumn 2019 and unusually high temperatures in summer 2021) illustrated how episodic disturbances can drive substantial shifts in microbial composition; notably, Synechococcus became particularly prevalent after the intense rainfall event. Fine‑scale analyses of 16S rRNA and petB gene variants revealed that a restricted set of Synechococcus lineages dominated throughout the study period. Comparative genomic analyses of these cyanobacterial populations highlighted distinct functional repertoires, including genes involved in osmoprotectant biosynthesis, diverse toxin-antitoxin systems, herbicide resistance, and multiple viral defense mechanisms, present only in specific variants. Finally, temporal analyses of viral assemblages indicated that cyanophages played a key role in modulating Synechococcus population dynamics. Conclusions: The temporal dynamics of prokaryotic communities in the Mar Menor indicate that the lagoon remains in an altered, non‑equilibrium state, likely sustained by recurrent anthropogenic and climatic pressures. The contrasting microbial responses observed during two different deoxygenation events underscore the ecosystem’s complexity. This study highlights the importance of incorporating microbial community analyses into long‑term monitoring of threatened coastal systems, and the power of comparative genomics for identifying functional traits that enable cyanobacterial proliferation in disturbed ecosystems.

We analyzed the changes in protist biodiversity and community structure in the coastal lagoon of the Mar Menor after the phytoplankton bloom that produced the collapse of the ecosystem in 2016. The analyses were based on a time series of 18S ribosomal RNA gene metabarcoding data covering from Aug-2016 to Jun-2018. Relative abundances of amplicon sequence variants (ASVs) assigned at least to order level were categorized into four tropic modes (autotrophic, dinoflagellates, heterotrophic, and Syndiniales) and used for network analyses based on co-occurrence matrices. This post-bloom period was characterized by large fluctuation in phytoplankton biomass, including phases with chlorophyll (Chl) a concentrations lower than 1.0 mg L-1 and peaks above 12.7 mg L-1. Cluster and NMDS analyses permitted distinguishing three communities featuring periods with different productivity level. ASVs assigned to the four trophic modes contributed significantly to these differences. Comparisons among the networks built for each period showed that average degree and stability changed with the Chl a levels of the lagoon; specifically, low productivity conditions lead to higher stability. These changes in network topology occurred together with changes in the number of modules that increased during the period of highest productivity implying a reshuffling of the networks into sub-networks (modules) of ASV dense aggregates. Since centrality was lower during low Chla a concentration periods, the higher modularity at high Chl a concentration implies that the network is re-organized around a comparatively smaller amount of ASVs, which are strongly connected and might lead to higher vulnerability. Our results support the hypothesis that plankton network structure is modulated by changes in nutrient levels, emphasizing the importance of trophic interactions in shaping the plankton community’s response. Our work underscores the importance of considering the entire protist communities in eutrophication surveillance programs.

Aerobic anoxygenic phototrophic (AAP) bacteria play an important role in ocean biogeochemistry by degrading organic matter and capturing light energy through bacteriochlorophyll a. However, how their genetic and ecological traits vary with lifestyle remains underexplored. We investigated free-living (FL) and particle-associated (PA) AAP communities and their responses to environmental variability in the northern Alboran Sea. Surface seawater was collected during seven cruises conducted in spring, autumn, and winter, each covering four coast-to-offshore transects. AAP abundance was quantified by infrared epifluorescence microscopy, and community diversity was assessed using pufM gene amplicon sequence variants (ASVs). AAP abundance was significantly higher in spring than in winter, although no consistent spatial pattern was observed. PA communities exhibited greater diversity than FL communities. Around 65% of ASVs were unique to the PA fraction, although most of these were rare. Distinct AAP phylogroups displayed clear niche preferences: PA-associated groups were more common in coastal waters, whereas FL groups predominated offshore. Both communities showed pronounced seasonality, but spatial structuring along the west-to-east gradient was more apparent in FL than in PA communities. Environmental drivers also differed between lifestyles, with salinity primarily shaping FL communities and chromophoric dissolved organic matter influencing PA communities. Our results indicate that lifestyle (FL vs. PA) is a major determinant of AAP bacterial diversity, spatiotemporal patterns, and environmental responses.

Coastal lagoons are highly productive ecosystems, yet their prokaryotic viruses remain poorly studied. The Mar Menor, a hypersaline coastal lagoon in south-eastern Spain, is under strong anthropogenic pressure from continuous agricultural runoff, leading to severe eutrophication. To assess the impact of these unique conditions on viral assemblages, we analyzed a 3-year metagenomic time series of picoplankton communities. We reconstructed the lagoon’s prokaryotic DNA viral communities and compared them with their counterparts in open Mediterranean Sea waters to reveal how environmental variability shapes their structure. Viral communities in the Mar Menor showed higher viral operational taxonomic unit relative abundances and diversities and were distinct from those offshore. Temporally, community structure was correlated with water transparency and silicate concentration. The putative hosts of the lagoon viruses were copiotrophic rather than oligotrophic compared to the open sea, and their composition shifted in response to episodic environmental disturbances. Temperate virus levels did not consistently support either the piggyback-the-winner or refugium models, spatially or temporally, indicating that viral replication strategies are governed by factors more complex than trophic status or environmental variability alone. Auxiliary viral genes (AVGs) encoding 2-oxoglutarate/Fe(II)-dependent oxygenase and DNA methyltransferase emerged as potentially relevant functions in the lagoon, as they were more frequent than in the Mediterranean Sea. Similar to targeted hosts, AVG-specific temporal relative abundance patterns were strongly shaped by local disturbances. This study provides the first metagenomic insight into viruses of the Mar Menor, revealing viral ecology in a dynamic, eutrophic lagoon, with implications for predictive models of nutrient cycling.

The Asian brown macroalga Rugulopteryx okamurae has invaded the oligotrophic areas of Mediterranean coasts since 2015, with drastic impacts on environmental conditions and socioeconomic activities in coastal areas in Europe. Therefore, it is intriguing how this species is able to grow and expand at the observed rates. In this context, the physiological responses of R. okamurae to changing nutrient concentrations and temperature were analyzed. Two experiments were conducted, evaluating six combinations of nitrate and phosphate concentrations and their potential interaction with temperature. Nutrient uptake efficiency (NUE) and rates (NUR), photosynthetic responses, growth rates, and biomass composition were evaluated. Photosynthesis parameters, soluble proteins, and ‐NUR increased with increasing N:P ratio; however, ‐NUR was very similar in all treatments. The species showed high capacity for nitrate assimilation, which was rapidly modulated by its external concentration and temperature (more than 90% of NO₃‐NUE after 5 days in treatments with N:P rations of 5, 10, 16, 25, and 40 N to 1 P). Consequently, N‐nutrients were removed from the water by R. okamurae and likely stored inside the cells. This process will allow the alga to maintain high growth rates if thalli are moved to oligotrophic areas, favoring its spreading to many marine environments. Additionally, fucoxanthin was the predominant carotenoid in this species, although its content was lower than in other brown macroalgae species (mean value of 0.51 ± 0.05 mg · g⁻¹ DW). However, since a huge amount of R. okamurae is observed recurrently on beaches, the use of this biomass might be proposed to compensate partially for its impacts.

Aerobic anoxygenic phototrophic (AAP) bacteria are a common part of microbial communities in the sunlit ocean. They contain bacteriochlorophyll a (BChl a)‐based photosystems that harvest solar energy for their metabolism. Across different oceanic regions, AAP bacteria seem to be more abundant in eutrophic areas, associated with high chlorophyll concentrations. While most previous studies focused on surface samplings, there is limited information regarding their vertical distribution in euphotic zones of the major ocean basins. Here, we hypothesized that AAP bacteria will follow a similar structure to the chlorophyll depth profile across areas with different degrees of stratification. To test this hypothesis, we enumerated AAP cells and determined bulk water BChl a concentrations along the photic zone of a latitudinal transect in the South and Central Atlantic Ocean. Overall, the distribution of AAP bacteria was highly correlated to that of chlorophyll a and to the abundance of picophytoplankton across both vertical and horizontal gradients. Furthermore, estimated light energy captured across the water column showed that, while AAP bacteria share a common latitudinal pattern of light absorption with picophytoplankton, they display a unique vertical arrangement with highest photoheterotrophic activity in the top 50 m of the surface ocean.