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Diversity of protists was researched in different coastal areas of the Mediterranean Sea by means of high throughput sequencing technologies based on the amplification of a specific region of the 18S rRNA gene. A total of 25 samples were obtained in the Mar Menor coastal lagoon (MMS) in 2016-2017 after the ecosystem suffered a so-called 'ecosystem disruptive algal bloom' which was attributed to nitrate pollution. Another set of samples (9) was harvested in 2018 at a coastal area of the northern Alboran Sea, which received urban wastewater (CS). The community structure in these two areas was compared with samples collected at stations of the Alboran Sea following a trophic gradient from coast to open sea (UP; 15 samples; OAS) located far from pollution sources. On average, Alveolata, Stramenopila and Rhizaria counted for more than 85% of the total sequence reads in the three areas although the contribution of the three groups was different. The relative abundance of Alveolata reads averaged 62% in OAS but increased notably in CS (80%) and MMS (70%). In contrast, both diversity and abundance of Rhizaria were reduced in CS (1.4% and 4.7% of reads and OTUs) and MMS (3% and 7%) compared to OAS (5.5% and 9.7%). The highest contribution of Stramenopila to total reads was obtained in OAS (20% compared to 8% and 13% in CS and MMS, respectively). a-diversity of autotrophs, dinoflagellates and heterotrophs decreased in the areas impacted by nutrient pollution. However, these was not a consistent variability pattern in b-diversity.

Microplankton is an heterogeneous group of organisms ranging between 20 and 200 microns in size. Morphological characterization of its diversity is challenging as it includes Chromista, Protozoa, and Metazoa (adults and larvae). We characterized the composition of the microzooplankton community (heterotrophic and mixotrophic) collected with a CalVET net (50 µm mesh), in a coastal area affected by urban wastewater discharges in the N Alboran Sea (SW Mediterranean). We applied an integrative taxonomic approach, combining metabarcoding of the mtDNA cytochrome oxidase I (COI) and the V4 region of the 18S rRNA (18S) genes with morphological microscopic identification of organisms. Both methods showed differentiated coastal and offshore microzooplankton assemblages. The dominant taxa varied depending on the method used, with Dinophyceae accounting for 64-85% of the microscopy counts but Arthropoda representing up to 98% or the COI and 18S reads. When computing Protozoa and Metazoa relative abundances separately, both microscopy and metabarcoding revealed unicellular communities dominated by thecate Dinophyceae, followed by Ciliophora. Metazoa microscopy counts were dominated by eggs, followed by Copepoda nauplii in offshore waters, whilst by Appendicularia and Mollusca larvae in the shallow coastal stations. COI reads also corresponded mostly to Copepoda and Mollusca. However, 18S reads were dominated by Thecostraca and Copepoda. Despite the identification level differed among methods and taxa, the integrated approach revealed higher diversity than expected.

Copepods are the main prey for small pelagic fishes. Despite their commercial importance, little is known about the predator-prey interactions and their role in the trophic web dynamics. Traditional characterization of copepods is achieved through microscopy, with the inherent caveats of cryptic species misidentification and lack of specificity for some young stages. In trophodynamic studies, identification of copepods within the predators gut is not easy, specially when the organisms are partly digested and/or correspond to larval stages. Still, this knowledge is key to understand and to provide advice for a sustainable management of the marine resources. Important advances in molecular tools have been achieved to facilitate copepods identification, and several molecular markers have been applied to characterize copepods diversity with different results. However, to date, microscopic identification is still much needed to evaluate molecular procedures. In the case of small pelagic fishes, such as sardine and anchovy, larval diet studies are challenging as they prey mostly on microplanktonic organisms. An integrative taxonomic approach, combining microscopy and molecular techniques, is explored to assess the contribution of copepods and their larvae to the diet of commercially important fish species.

Zooplankton play a central role in marine trophic webs, influencing both biogeochemistry and productivity of the oceans. Changes in their communities are important indicators of overall ecosystem health and global change impacts. With increasing exploitation and pressures on the marine environment, there is a growing need for high-resolution monitoring of marine zooplankton to provide detailed information about seasonal to decadal changes at local, regional, and global scales. This crucial knowledge is gathered mainly through long-term time series, which are key to characterizing and forecasting changes in marine zooplankton assemblages. In this Introduction, and through the articles included in this Themed Article Set, we bring together new insights, issuing from data time series, into zooplankton population dynamics.We also take up the application of such time series to the understanding of global change impacts on marine ecosystems and in providing advice on sustainable management of marine ecosystem resources and services. We highlight the importance of maintaining and supporting long-term marine zooplankton time series as key contributors to the development and advancement of the United Nations’ Decade of Ocean Science for Sustainable Development Goal 13-Climate action and Goal 14-Life below water.

Zooplankton are the main prey for small pelagic fishes. The most common small pelagic fish species in the Alboran Sea (SW Mediterranean Sea) is the European sardine (Sardina pilchardus). Despite its commercial importance in the region, little is known about its larval trophodynamics and the role that zooplankton play in their recruitment success. Microscopic characterization of the larval gut contents is challenging as they prey mostly on partly digested microplanktonic organisms. Several molecular tools have been developed that may overcome this caveat. The gut content of sardine larvae (6 - 21 mm standard length) collected over a diel cycle in the Northern Alboran Sea was analyzed by mitochondrial COI metabarcoding, and compared with the field zooplankton community composition. Diel variability was observed in zooplankton relative abundances, both in the larval gut contents and in the field. Sardine larvae preys included several copepod nauplii, but also DNA of cladocera, euphausiid, gastropod and hydrozoa was detected, suggesting an opportunistic foraging behavior, instead of a selective diet.

Variability in composition and structure of the mesozooplankton communities in the Bay of Malaga (SW Mediterranean) were characterized during a 26 h cycle using an integrative taxonomic approach. We combined microscopic identification of organisms, with metabarcoding for the genes of the mitochondrial DNA COI and the V9 hypervariable region of the ribosomal RNA 18S. Richness and diversity obtained by microscopy were higher than those measured with COI, as COI did not detect some phyla. COI however allowed for the identification to species level of several taxa that were left at higher taxonomic rank under the microscope. 18S detected a wider range of taxa than COI and microscopy, although with lower taxonomic resolution. Differences between coastal-night and shelf-day zooplankton communities structure were detected by both microscopy and metabarcoding. The combination of these two approaches increased the known copepod species in the SW Mediterranean Sea by 9%. An integrative approach combining morphology and COI metabarcoding is proposed to further facilitate mesozooplankton biodiversity studies.

The Mediterranean Sea is subjected to strong anthropogenic pressures that may be causing important ecosystem changes, particularly in coastal areas under high anthropogenic pressure. We characterized the composition of the microzooplankton community in a coastal area in the N Alboran Sea (SW Mediterranean) highly impacted by urban wastewater pollution. Two offshore outfalls release urban wastewater to the sea at a 40 m bottom depth, from a nearby town. We applied an integrative taxonomic approach, combining metabarcoding of the mitochondrial COI and the 18S rRNA genes with morphological microscopic identification of organisms, collected with a CalVET net (50 µm mesh). Hydrology was notably affected near the bottom at the vicinity of the submarine emissaries exit, presenting increased temperature and turbidity, and decreased salinity due to the urban freshwater discharge. Nutrient concentrations exceeded the Water Framework Directive limits; however, chlorophyll a concentrations were not very high, due to strong water column stratification. Microzooplankton communities (50-200 µm) were dominated by dinoflagellates (50-80% relative abundance), followed by copepods (copepodites and nauplii), eggs and cysts. We found significant differences in communities’ composition between the coastal shallow area and the offshore waters, driven by pollution and stratification.

Variability in the spatial and temporal distribution of the mesozooplankton abundance in the N Alboran Sea (SW Mediterranean) was assessed intermittently from 2010 to 2020, and compared with 1992–2000 historical time series data. Total abundance of mesozooplankton was significantly higher in the coast than in the shelf and slope waters. There were significant differences in mesozooplankton abundance between 1992–2000 and 2010–2020 at the three zones. Copepods dominated the mesozooplankton during winter and spring, but cladocerans and doliolids also became important components of the community in summer and autumn. We found significant increases between the first and the second decadal periods in the abundance of copepods, appendicularians, holoplanktonic gastropods and siphonophores in the shelf. However, in the coast, copepod nauplii, doliolids, gastropods and siphonophores increased, while euphausiids abundance decreased significantly. These trends contrast with the ongoing decline of the sardine stocks in European waters. Increasing temperature and decreasing predation pressure are suggested to be the main drivers of mesozooplankton variability.

An investigation on microplankton composition and spatial distribution has been carried out around Italian seas. The analysis of 53 samples, collected in 2017 at two depths in 27 different stations, has led to a scenario of horizontal distribution of microplankton. Dinophyta and Ciliophora were chosen as representatives of the whole microplankton community. A total of 60 genera were identified. Cluster analysis of data regarding taxa presence and abundance led us to recognize that similarities between surface stations were more evident than those between deep ones. Furthermore, we conducted an inter-annual comparison with available data from the South Adriatic Sea (2013, 2015). The higher dissimilarity between deep sea samples was also confirmed in a relatively smaller geographic area. The dissimilarity of deep-sea samples does not correspond to a higher habitat diversification, in terms of abiotic parameters. It has been suggested that the negligible biological connectivity in the deep, for those micro-organisms not able to perform wide spatial migrations, could produce such a biological diversification

We investigated aminoacyl-tRNA synthetases (AARS) activity and individual growth rate (IGR) as individual-based in situ indicators of growth in adult krill, Euphausia pacifica. AARS enzymes catalyze the first step in protein synthesis while the IGR method is based on changes in body length during molting. Growth rates of field-collected krill were measured via the IGR method and individuals were subsequently preserved for AARS analysis to yield paired measurements. Our results show that conditions during the IGR incubation period influenced AARS activity in these individuals precluding a direct comparison but revealing the different timescales across which these two measures integrate. Importantly, they show that AARS activity provides a snap-shot image of an organism's metabolism, while IGR of krill is thought to integrate their environmental experience over several days. Each method would require repeated measurements to estimate population growth rates integrated over seasonal or generational time scales. As part of this project, we investigated how specific the AARS assay is to protein synthesis by testing a modified protocol that includes an additional blank and found evidence that the current assay may be measuring other cellular processes in addition to its intended signal. Our results suggest that a new NADH Blank might be optimized to improve the specificity of the assay.

The northern coasts of the Alboran Sea are known to have thrived from past artisanal fisheries that exploited the early life stages of fishes. This was mainly carried out by a suite of different fishing gears dating back to the eighteenth century to the end of the twentieth century (Sañez-Reguart 1791–1795 reprint 1988; Rodríguez Santamaría 1923). These fishery studies provide detailed descriptions of the fishing gears employed by fishermen exploiting the Iberian Peninsula coasts and a general account of the targeted species and their associated catches. In the Andalusian coasts of the Alboran Sea, beach seines called boliches were among the most common, targeting on sardines, anchovies, and a number of other fish species, as bonitos and tunas that preyed on small pelagic shoals

Despite demersal trawling monitoring programs are not aimed at quantifying mesopelagic organisms, they are recurrently captured as by catch between 30 and 800 m depth. These species are mostly diel vertical migrants, with differentiated behavior from benthic and demersal ones. Nevertheless, they are sometimes captured in large quantities (both abundance and biomass) although absent on other occasions. The co-occurrence observed with demersal populations may probably be due to the daytime and location of samplings, i.e. depth and type of bottom (habitat). In order to understand the mesopelagic-demersal coupling, we discuss spatio-temporal patterns observed along the Spanish Mediterranean coast during the 1994-2012 MEDITS survey.

The northern coasts of the Alboran Sea are known to have thrived from past artisanal fisheries that exploited the early life stages of fishes. This was mainly carried out by a suite of different fishing gears dating back to the eighteenth century to the end of the twentieth century (Sañez-Reguart 1791–1795 reprint 1988; Rodríguez Santamaría 1923). These fishery studies provide detailed descriptions of the fishing gears employed by fishermen exploiting the Iberian Peninsula coasts and a general account of the targeted species and their associated catches. In the Andalusian coasts of the Alboran Sea, beach seines called boliches were among the most common, targeting on sardines, anchovies, and a number of other fish species, as bonitos and tunas that preyed on small pelagic shoals (Fig. 13.1).

The diversity of protists was researched in the Alboran Sea (SW Mediterranean Sea) by means of high-throughput sequencing technologies based on the amplification of the V9 region of 18S rRNA. Samples were collected at different depths in seven stations following an environmental gradient from a coastal upwelling zone to the core of an oligotrophic anticyclonic gyre (AG). Sampling was performed during summer, when the water column was stratified. The superphyla Alveolata, Stramenopila and Rhizaria accounted for 84% of the total operational taxonomic units (OTUs). The most diverse groups were Dinophyceae (21% of OTUs), Marine Alveolates-II (MALV-II; 20%), Ciliophora (9%) and MALV-I (6%). In terms of read abundance, the predominant groups were Dinophyceae (29%), Bacillariophyta (14%), MALV-II (11%) and Ciliophora (11%). Samples were clustered into three groups according to the sampling depth and position. The shallow community in coastal stations presented distinguishable patterns of diatoms and ciliates compared with AG stations. These results indicate that there was a strong horizontal coupling between phytoplankton and ciliate communities. Abundance of Radiolaria and Syndiniales increased with depth. Our analyses demonstrate that the stratification disruption produced by the AG caused shifts in the trophic ecology of the plankton assemblages inducing a transition from bottom-up to top-down control.

The Alborán Sea sardine (Sardina pilchardus) is the most abundant small pelagic fish in the Mediterranean Sea. Along the northern coast of the Alborán Sea, Málaga and Almería Bay are two important nursery grounds with contrasting oceanographic characteristics. Post-larval stages of S. pilchardus were collected during the late autumn and late winter along with the mesozooplankton community. We examined the influence of feeding behavior on larval growth using environmental variables, daily growth metrics, otolith biometry, stable isotope analysis and trophodynamics. Trophic positions were calculated using mesoozooplankton as potential prey for S. pilchardus. During both seasons, we observed faster growth in larger otoliths that also corresponded to higher trophic positions. Our results indicate that the isotopic signature of larvae is highly influenced by the mesozooplankton community structure. Moreover, the trophic variables showed a significant linear relationship with the estimated ages for all larvae indicating dietary changes throughout ontogenic development.

The influence of hydrochemistry and trophic conditions on the coastal zooplankton community’s biomass and metabolic activities was investigated along the Spanish Mediterranean coastal waters, from Algeciras Bay to Barcelona, from autumn 2011 to autumn 2012. Two hydrographic regions were differentiated: NW Alboran (ALB) and W Mediterranean (MED). Zooplankton metabolism was assessed from measurements of the electron transport system (ETS) and aminoacyl-tRNA synthetases (AARS) activities, as proxies for potential respiration and somatic growth, respectively. Zooplankton showed three to fivefold higher biomass in ALB than in MED during autumn 2011 and spring 2012. However, in autumn 2012, a drastic decrease in biomass standing stock was observed in ALB, with no significant differences between the two regions. This biomass depletion event was not associated with environmental variables, food availability or zooplankton metabolic rates, but coincided with a twofold peak of Sardina pilchardus landings in ALB. A reduced standing stock coupled with high zooplankton growth rates suggests mortality by predation as the main cause for the low zooplankton biomass typically observed in MED, and in ALB during autumn 2012.

To assess the likely economic outcomes to fishing fleets of the Landing Obligation (LO), bioeconomic models covering seven European fisheries, ranging from the North East Atlantic to the Mediterranean, have been applied to estimate the economic performance of fleets before and after implementing the LO. It is shown that for most of the analysed fisheries, their economic outcome will be negatively affected in the long term by the LO, when compared to the expected outcome with no LO. Efficient mitigation strategies (exemptions, quota uplifts, improved selectivity, effort reallocation and others) may, for some of the analysed fisheries, reduce the negative economic effect of the LO. Moreover, the possibility to trade quotas, both nationally and internationally, may also reduce the economic losses caused by the LO. However, even with mitigation strategies and/or quota trade in place, most of the analysed fisheries are worse off under the LO than what could be expected if the LO was not implemented.