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Morphological and genetic investigations have led to the identification of Spiophanes adriaticus sp. nov. (Polychaeta: Spionidae) from the North Adriatic Sea (Central Mediterranean). A total of 81 specimens were recorded along the sublittoral zone between 8 and 27.5 m of depth. This species differs from other congeners by having: two pairs of black eyes, a cirriform occipital antenna, dorsal ciliated organs as thin bands usually extending to chaetigers 11–12, dorsal ciliated crests from chaetiger 14–17, undulate glandular opening on chaetigers 5–7, unhooded hooks from the 15th chaetiger and Y shaped tubes. A detailed description and illustrations are provided for the new species. Through DNA barcoding results and comparison of DNA sequences of the new species with those of other congeners available in the GenBank database, the validity of the new finding was confirmed. Spiophanes adriaticus sp. nov. represents the eighth species of Spiophanes recorded for the Mediterranean Sea. A key for the identification of Mediterranean Spiophanes species is also provided.

We assessed the effect of sewage-derived materials on the structural and functional attributes of the soft-bottom macrofauna at an increasing distance from the entire diffusion area. Our results showed clear spatial changes of macrofaunal density and biomass along the distance gradient from the main outfall. High values of biodiversity, species composition, and species linked to organic enrichment near the duct suggested that moderate organic stress affected this community. The traits analysis abundance-based, compared to biomass-based one, distinguished most clearly sewage contamination conditions. Functional diversity displayed spatial patterns with higher values in the less impacted sites and was significantly related to species numbers and the biotic indices (like M-AMBI). This approach is ideal for detecting macrofaunal functional changes due to sewage contamination. Thus, we infer that traits analyses could offer great potential for environmental assessment and monitoring of coastal areas influenced by human activities.

Benthic prokaryotes are the key-players in C-cycling at the sediment-seawater interface, one of the largest biologically active interfaces on Earth. Here, microbial-mediated processes, such as the degradation of organic matter and the incorporation of mobilized C into microbial biomass, depend on several factors such as environmental temperature and substrate availability, especially in shallow sediments at mid-high latitudes where seasonal fluctuations of these variables occur. In the present study, four degradative activities (β-glucosidase, lipase, chitinase and aminopeptidase), Heterotrophic C Production (HCP), Total Organic C (TOC), Total Nitrogen (TN) and Biopolymeric C (BPC) were investigated seasonally from April 2010 to April 2018 in the surface sediments of a shallow Long-Term Ecological Research (LTER) station of the northern Adriatic Sea. Significant temperature-dependences were described by Arrhenius-type equations for HCP and each of the degradative activities tested with the exception of aminopeptidase. The relatively low apparent Activation Energies suggested that these microbial-mediated processes were enhanced by the availability of palatable substrates over the study period. Nevertheless, a clear and tight dependence from such substrates was detected only for aminopeptidase, the most pronounced degradative activity observed. TN was identified by the stepwise multiple regression analysis as the environmental variable that mainly drove this exoenzymatic activity. Enhanced aminopeptidase rates mirrored peaks of TN that seemed, in turn, linked to the seasonal proliferation of benthic microalgae. By supplying prokaryotes with promptly available substrates, these autotrophs, represented mainly by diatoms, seemed to play an important role in the C-cycling regulation at the studied LTER station.

Marine heterotrophic prokaryotes degrade, transform, and utilize half of the organic matter (OM) produced by photosynthesis, either in dissolved or particulate form. Microbial metabolic rates are affected by a plethora of different factors, spanning from environmental variables to OM composition. To tease apart the environmental drivers underlying the observed organic matter utilization rates, we analysed a 21 year-long time series from the Gulf of Trieste (NE Adriatic Sea). Heterotrophic carbon production (HCP) time series analysis highlighted a long-term structure made up by three periods of coherent observations (1999-2007; 2008-2011; 2012-2019), shared also by OM concentration time series. Temporal patterns of HCP drivers, extracted with a random forest approach, demonstrated that a period of high salinity anomalies (2002–2008) was the main driver of this structure. The reduced river runoff and the consequent depletion of river-borne inorganic nutrients induced a long-term Chl a decline (2006–2009), followed by a steady increase until 2014. HCP driving features over the three periods substantially changed in their seasonal patterns, suggesting that the years following the draught period represented a transition between two long-term regimes. Overall, temperature and particulate organic carbon concentration were the main factors driving HCP rates. The emergence of these variables highlighted the strong control exerted by the temperature-substrate co-limitation on microbial growth. Further exploration revealed that HCP rates did not follow the Arrhenius’ linear response to temperature between 2008 and 2011, demonstrating that microbial growth was substrate-limited following the draught event. By teasing apart the environmental drivers of microbial growth on a long-term perspective, we demonstrated that a substantial change happened in the biogeochemistry of one of the most productive areas of the Mediterranean Sea. As planktonic microbes are the foundation of marine ecosystems, understanding their past dynamics may help to explain present and future changes.

This study aims to validate the stable carbon isotopic composition (&delta, 13C) of phytoplankton as a tool for detecting submarine leakages of anthropogenic CO2(g), since it is characterised by &delta, 13C values significantly lower than the natural CO2 dissolved in oceans. Three culture experiments were carried out to investigate the changes in &delta, 13C of the diatom Thalassiosira rotula during growth in an artificially modified medium (ASW). Three different dissolved inorganic carbon (DIC) concentrations were tested to verify if carbon availability affects phytoplankton &delta, 13C. Simultaneously, at each experiment, T. rotula was cultured under natural DIC isotopic composition (&delta, 13CDIC) and carbonate system conditions. The available DIC pool for diatoms grown in ASW was characterised by &delta, 13CDIC values (&minus, 44.2 &plusmn, 0.9&permil, ) significantly lower than the typical marine range. Through photosynthetic DIC uptake, microalgae &delta, 13C rapidly changed, reaching significantly low values (until &minus, 43.4&permil, ). Moreover, the different DIC concentrations did not affect the diatom &delta, 13C, exhibiting the same trend in &delta, 13C values in the three ASW experiments. The experiments prove that phytoplankton isotopic composition quickly responds to changes in the &delta, 13C of the medium, making this approach a promising and low-impact tool for detecting CO2(g) submarine leakages from CO2(g) deposits.

Evaluating the effects of anthropogenic pressure on the marine environment is one of the focal objectives in identifying strategies for its use, conservation and restoration. In this paper, we assessed the effects of chemical pollutants, grain size and plastic litter on functional traits, biodiversity and biotic indices. The study was conducted on the benthic communities of three harbours in the central Mediterranean Sea: Malta, Augusta and Syracuse, subjected to different levels of anthropogenic stress (high, medium and low, respectively). Six traits were considered, subdivided into 22 categories: reproductive frequency, environmental position, mobility, life habit, feeding habit and bioturbation. Functional diversity indices analysed were: Functional Divergence, Quadratic Entropy, Functional Evenness and Functional Richness. To assess the trait responses to environmental gradients, we applied RLQ analysis, which considers simultaneously the relationship between three components: environmental data (R), species abundances (L) and species traits (Q). From our analyses, significant relationships (P-value = 0.0018 for permutation of samples, and P-value = 0.00027 for permutation of species) between functional traits and environmental data were highlighted. The trait categories significantly influenced by environmental variables were those representing feeding habits and mobility. In particular, the first category was influenced by chemical pollutants (organotin compounds and polycyclic aromatic hydrocarbons) and grain size (silt and sand), while the latter category was influenced only by chemical pollutants. Pearson correlations performed for functional vs biotic and diversity indices confirmed the validity of the chosen conceptual framework for harbour environments. Finally, linear models assessing the influence of stressors on functional parameters underlined the link between environmental data vs benthic and functional indices. Our results highlight the fact that functional trait analysis provides a useful and fast method for detecting in greater depth the effects of multiple stressors on functional diversity in marine ecosystems.

Marine benthic microalgae are a promising bioindicator of contamination. To date, however, investigations on the microbenthic communities subjected to multiple stressors in natural environments are still very rare. To assess whether the benthic processes of primary production and oxygen consumption, and the structure of active and resting microbenthos, were affected by sediment contamination, seven stations were sampled in different zones of the port of Trieste, subjected to multiple and diffuse contamination, and a reference site in the Marine Reserve of Miramare. No major differences in total abundance of active microbenthos were observed among sites, but the dominance of stress-resistant species and the reduction of more sensitive ones, were registered nearby the main productive activities. The densities of resting microbenthos were higher in polluted areas, and represented by key dinoflagellate species that were clearly linked to contamination. The analysis of similarity applied to both active and resting communities significantly separated the most contaminated stations from the other ones. The photosynthetic capability of active microbenthos did not seem to be affected by contamination. The maximum oxygen consumption rates observed in sediments nearby the productive activities were likely ascribable to high organic C contents and the presence of metals in reduced chemical form.

Antarctic polynyas are among the most productive areas in the ocean. They are subjected to strong temporal variations, having profound effects on the local ecosystems. We tested the changes occurring in several biogeochemical features [Chlorophyll a (Chl a), phaeopigment, dissolved and particulate organic carbon (DOC and POC) concentrations] as well as in biological dynamics (prokaryotic and nanoplanktonic abundance, heterotrophic carbon production and degradative activities) at the transition between late spring and summer in surface waters (upper 125 m) in the Terra Nova Bay polynya, in the Ross Sea. Samplings were performed from January 18 to 21 and, after an interval of almost 5 days, from January 25 to 27. The first period was characterised by spring conditions still maintained by the presence in the area of two mega-icebergs (B15 and C19), which caused a delay in the ice melting that started during the second survey. Chlorophyll a concentrations were highest during the first period, whereas phaeopigments/Chl a ratio increased during the following sampling time suggesting variations in phytoplankton biomass/physiology and a change in organic matter (OM) quality. No significant differences in DOC and POC concentration were detected between the two periods together with unvaried abundances of prokaryotes and small protists. The changes in OM over time were evidenced also by changing exoenzymatic activity patterns. Notwithstanding the general variations occurring during the surveys, heterotrophic production and prokaryotic growth were not substantially modified, suggesting a rapid (timescales of days) acclimation to changing organic matter quality for the maintenance of prokaryotic metabolic requirements.

Understanding the ecosystem functioning in the dark portion of the ocean is a challenge that microbial ecologists are still facing. Due to the large volume, the global deep Ocean plays a central role in the regulation of climate, possibly buffering the rise of atmospheric carbon dioxide if processes of CO2 fixation compensate for respiration. We investigated the rates of several prokaryotic activities (dissolved and particulate primary production, heterotrophic carbon production and respiration) in meso- and bathypelagic waters of the Mediterranean Sea, covering all sub-basins. Chemosynthesis was the main process for C uptake. The rates of organic C (OC) excretion (or viral-induced cell lysis) inferred from the dissolved primary production measurements were noteworthy, being comparable to particulate primary production, and possibly contributing to the formation of non-sinking particulate organic matter. Inorganic C fixation rates were significantly higher than those reported for other deep-sea systems, probably as a consequence of the persistently higher temperature of dark Mediterranean waters or to phylogenetically diverse communities involved in the process. Primary production was negatively correlated with dissolved organic carbon concentration and showed an inverse pattern to heterotrophic carbon production, indicating a niche partitioning between heterotrophs and autotrophs. In sum, the deep Mediterranean Sea harbors active autotrophic communities able to fix inorganic carbon faster than the heterotrophic carbon production rates.

In the northern Adriatic Sea (the northernmost basin of the Mediterranean Sea) wind forcing plays a key role in shaping the water column structure, circulation patterns and dense water formation. The latter process might be enhanced during winter by local north-easterly wind, the Bora, responsible for intense and long-lasting episodic outbreaks. Although outbreaks of Bora are extensively studied in the context of thermohaline circulation, little is known about their effects on planktonic microbial communities. From late February to early March 2018, a persistent and strong Bora event caused an unusual drop of seawater temperature (down to 5.7 °C) in the Gulf of Trieste. To investigate the effect of this extreme meteorological event on the coastal planktonic microbes, we evaluated changes in their abundance and cytometric fingerprinting, heterotrophic carbon production rates and the activity of six exoenzymes (β-glucosidase, β-galactosidase, chitinase, lipase, alkaline-phosphatase and leucine aminopeptidase). Additionally, we set up temperature manipulation experiments to investigate the potential limiting effect of the temperature drop on microbial degradation and uptake of organic matter. The dataset clustered in two distinct groups: a cold-affected period (26th February - 8th March), characterised by a reduced particulate organic matter availability and slow metabolic rates, and a recovery one, (12th - 16th March) defined by an overall increase of substrate availability and enhanced heterotrophic carbon production and hydrolysis rates. Our findings revealed that the exoenzymatic activities were constrained at their lower thermal limit during the cold-affected period and that, deviating from the Arrhenius’ linear response to temperature, the prokaryotic growth was limited by the interactive effect of temperature and substrate availability. By limiting the microbial processing of organic matter, extreme meteorological events could alter the functioning of the entire planktonic compartment functioning for several days during and after the onset of the phenomenon, affecting the structure of local trophic webs.

Ports are subject to a variety of anthropogenic impacts, and there is mounting evidence of faecal contamination through several routes. Yet, little is known about pollution in ports by faecal indicator bacteria (FIB). FIB spatio-temporal dynamics were assessed in 12 ports of the Adriatic Sea, a semi-enclosed basin under strong anthropogenic pressure, and their relationships with environmental variables were explored to gain insight into pollution sources. FIB were abundant in ports, often more so than in adjacent areas; their abundance patterns were related to salinity, oxygen, and nutrient levels. In addition, a molecular method, quantitative (q)PCR, was used to quantify FIB. qPCR enabled faster FIB determination and water quality monitoring that culture-based methods. These data provide robust baseline evidence of faecal contamination in ports and can be used to improve the management of routine port activities (dredging and ballast water exchange), having potential to spread pathogens in the sea.

Regions of freshwater influence are affected by a constant interplay of different environmental factors that rule their seasonal and interannual highly variable dynamics. Riverine freshwater discharges alter the buoyancy of the local water masses, generating dynamic fronts and increasing water column stratification and nutrient availability. In such a heterogeneous context the paradigms for biological-physical interactions driving biogeochemical dynamics in the open seas do not always apply. We present here data from 12 surveys spanning 12 years (from 2004 to 2016) in the Po River prodelta area, which is highly representative of the above-described complexity, as it conveys the second largest freshwater discharge to the Mediterranean Sea. In particular, we focused on the microbially-mediated organic matter processing by estimating the numerical abundances of non-pigmented (‘heterotrophic’) and photoautotrophic (Synechococcus) prokaryotes, heterotrophic production and the activity of the exoenzymes beta-glucosidase, alkaline phosphatase and leucine aminopeptidase. The abundance of Synechococcus and heterotrophic prokaryotes as well as microbial activities were positively correlated to temperature and chlorophyll a concentration. Concomitantly, each variable was negatively correlated to salinity. In high-temperature, high salinity and low chlorophyll a samples, the heterotrophic production was limited and deviated from the typical linearity of the Arrhenius' law, suggesting resource limitation rather than temperature control. A multivariate analysis performed to analyze the pattern of organic matter degradation/utilization highlighted 11 distinct clusters of functional diversity. Temperature, salinity and chlorophyll a concentration data alone were able to explain most of the functional cluster separation as evidenced by a regression tree analysis. For freshwater-influenced samples, salinity was the only variable affecting metabolic patterns, whereas in typically marine waters, at salinity ≥37, metabolic profiles were determined by specific combinations of all 3 parameters.

This study represents the first example in which benthic heterotrophic and photoautotrophic microbial communities (prokaryotes and microphytobenthos-MPB, respectively) were simultaneously investigated. To explore how they synergistically respond to multiple natural and anthropogenic stressors, in the framework of the Project RITMARE four lagoons of the Po River Delta were sampled in May 2016: two with more marine features, i.e. Scardovari (SC) and Caleri (CL), and two more directly affected by the Po River flow, i.e. Canarin (CN) and Vallona-Marinetta (MV). The abundance and structure of benthic communities were related to physical-chemical parameters i.e. grain-size, total N, total organic C, stable C and N isotopes, and synthetic organic contaminants. Stations were gathered into three distinct groups (R-ansosim = 0.540 p < 0.001) according to their different physical-chemical features: outer, inner-freshwater and inner-marine sites. Contamination levels did not seem to severely affect the microbial abundances that were overall stimulated by the combined effect of high organic and nutrient loads: prokaryotes up to + 42% and MPB up to +93%. Bacteria and Archaea displayed high densities at sites directly influenced by the freshwater input and anthropogenically derived nitrogen. Delta- (30.8%), Alpha- (12.8%), Gamma- (11.8%) and Beta-Proteobacteria (7.1%) were the dominant classes at all sites. For both communities, a significant inter-lagoonal (among different lagoons) and infra-lagoonal (among stations within the same lagoon) pattern was highlighted by PERMANOVA. nMDS and SIMPER analyses revealed distinct assemblages in the inner and outer parts of the lagoons. We applied a novel functional approach based on diatom life modes. At inner and outer sites, different diatom living forms developed: epipsammic (on sand) nearby the lagoonal mouths, epipelic (on mud) at the innermost sites and non-benthic forms (planktonic, tychopelagic and epiphytic) at sites directly influenced by freshwater. Distance-based Linear Models further indicated that salinity, clay and temperature were the significant drivers of the prokaryotic spatial distribution whereas clay, PAHs, PCBs and salinity best explained the MPB structure. The dominance of non-benthic diatom life modes in the more polluted lagoon (CN) suggests a negative influence of contamination on the MPB structure. Two diatom keystone species likely contribute to restore the oxic gradient in sediments frequently exposed to anoxia, allowing the subsequent microbial aerobic degradation and the recolonization of higher trophic organisms. The capacity of re-oxygenation after anoxia has important ecological and economic implications in lagoons exploited for aquaculture.

A first synoptic and trans-domain overview of plankton dynamics was conducted across the aquatic sites belonging to the Italian Long-Term Ecological Research Network (LTER-Italy). Based on published studies, checked and complemented with unpublished information, we investigated phytoplankton and zooplankton annual dynamics and long-term changes across domains: from the large subalpine lakes to mountain lakes and artificial lakes, from lagoons to marine coastal ecosystems. This study permitted identifying common and unique environmental drivers and ecological functional processes controlling seasonal and long-term temporal course. The most relevant patterns of plankton seasonal succession were revealed, showing that the driving factors were nutrient availability, stratification regime, and freshwater inflow. Phytoplankton and mesozooplankton displayed a wide interannual variability at most sites. Unidirectional or linear long-term trends were rarely detected but all sites were impacted across the years by at least one, but in many case several major stressor(s): nutrient inputs, meteo-climatic variability at the local and regional scale, and direct human activities at specific sites. Different climatic and anthropic forcings frequently co-occurred, whereby the responses of plankton communities were the result of this environmental complexity. Overall, the LTER investigations are providing an unparalleled framework of knowledge to evaluate changes in the aquatic pelagic systems and management options.

The assessment of an ecosystem functioning is very complex and requires an integrated approach based on the combined and synoptic estimates of biological processes and the study of communities at different trophic levels. Here we present the main results gained over a 2 year-period aimed to investigate the benthic ecosystem functioning at a virtually pristine coastal site. Our suggested approach follows consecutive and interconnected steps: from the chemical characterisation of the sediments to the evaluation of the main autotrophic and heterotrophic metabolic processes, passing through the study of microphytobenthos and meiofauna. Our results indicate that in summer the system experienced pulsed inputs of fresh organic matter mostly due to the proliferation of benthic diatoms. This freshly produced material increased the sediment nutritional value supporting higher meiofaunal densities and stimulating benthic prokaryotes in mobilising C and incorporating it in new biomass. In winter, the lower availability of fresh organic matter, mainly due to the lower diatom abundances, contributed to a reduced prokaryotic C reworking and overall to a major confinement of C flow within the benthic microbial loop. The system shifted from net autotrophy to net heterotrophy as a response to temperature and light variations at the bottom. The latter factors directly influence the microalgal photosynthetic efficiency and are therefore responsible for the observed uncoupling between microphytobenthic abundances and primary production rates.

In this paper we investigated, for two years and with a bi-monthly frequency, how physical, chemical, and biological processes affect the marine carbonate system in a coastal area characterized by high alkalinity riverine discharge (Gulf of Trieste, northern Adriatic Sea, Mediterranean Sea). By combining synoptic measurements of the carbonate system with in situ determinations of the primary production (14C incorporation technique) and secondary prokaryotic carbon production (3H-leucine incorporation) along a river–sea gradient, we showed that the conservative mixing between river endmember and off-shore waters was the main driver of the dissolved inorganic carbon (DIC) distribution and seasonal variation. However, during spring and summer seasons also the influence of biological uptake and release of DIC was significant. In the surface water of June 2012, the spreading and persistence of nutrient-rich freshwater stimulated the primary production (3.21 μg C L− 1 h− 1) and net biological DIC decrease (− 100 μmol kg− 1), reducing the dissolved CO2 concentration and increasing the pHT. Below the pycnocline of August 2012, instead, an elevated bacterial carbon production rate (0.92 μg C L− 1 h− 1) was related with net DIC increase (92 μmol kg− 1), low dissolved oxygen concentration, and strong pHT reduction, suggesting the predominance of bacterial heterotrophic respiration over primary production. The flux of carbon dioxide estimated at the air–sea interface exerted a low influence on the seasonal variation of the carbonate system. A complex temporal and spatial dynamic of the air–sea CO2 exchange was also detected, due to the combined effects of seawater temperature, river discharge, and water circulation. On annual scale the system was a sink of atmospheric CO2. However, in summer and during elevated riverine discharges, the area close to the river's mouth acted as a source of carbon dioxide. Also the wind speed was crucial in controlling the air–sea CO2 exchange, with strong Bora events (a typical ENE wind of the Gulf of Trieste) that drastically increased the absorption (− 32.2 mmol m− 2 day− 1) or the release (5.34 mmol m− 2 day− 1) of carbon dioxide.

The effects of different physical and biogeochemical drivers on the carbonate system were investigated in a semi-enclosed coastal area characterized by high alkalinity riverine discharge (Gulf of Trieste, Northern Adriatic Sea, Mediterranean Sea). Our 2-year time-series showed that a large part of the seasonal carbonate chemistry variation was controlled by the large seasonal change of seawater temperature, though air-sea CO 2 exchange, biological activity (primary production-respiration), and riverine inputs also exerted a significant influence. With the exception of summer, the Gulf of Trieste was a sink of atmospheric carbon dioxide, showing a very strong CO 2 fluxes from atmosphere into the sea (−16.10 mmol m −2 day −1 ) during high wind speed event of north easterly Bora wind. The CO 2 influx was particularly evident in winter, when the biological activity was at minimum and the low seawater temperature enhanced CO 2 solubility. During spring, the drawdown of CO 2 by primary production overwhelmed the CO 2 physical pump, driving a significant decrease of dissolved inorganic carbon (DIC), [CO 2 ], and increase of pH T25 °C . In summer the primary production in surface waters occurred with the same intensity as respiration in the bottom layer, so the net biological effect on the carbonate system was very low and the further reduction of seawater CO 2 concentration observed was mainly due to carbon dioxide degassing induced by high seawater temperature. Finally, during autumn the respiration was the predominant process, which determined an overall increase of DIC, [CO 2 ], and decrease of pH T25 °C . This was particularly evident when the breakdown of summer stratification occurred and a large amount of CO 2 , generated by respiration and segregated below the pycnocline, was released back to the whole water column. Local rivers also significantly affected the carbonate system by direct input of total alkalinity (A T ) coming from the chemical weathering of carbonate rocks, which dominate the river watershed. Our finding clearly demonstrates a high A T concentration in low salinity surface waters (A T max = 2742.8 μmol kg −1 ) and a negative A T -salinity correlation. As a result the Gulf of Trieste revealed a low Revelle factor (10.1) and one of the highest buffer capacities of the Mediterranean Sea (s DIC = 0.31 mmol kg −1 ), which allows the system to store a significant amount of atmospheric CO 2 with a small decrease of seawater pH.

Marine aquaculture is the fastest growing sector of global food production and is projected to increase to meet future demand. Expansion and modernization of cultivation methods are needed to reach this target but a cost-benefit evaluation for biodiversity conservation is required to achieve sustainable aquaculture practices. We assess drivers of avian richness and abundance in a long-established seabird community present in a series of longline mussel farms in Italy and in response to a recent modernization process in the farming methodology. Over 2 years (24 surveys) we detected a remarkable diversity (15 species in 5 families) and abundance (n = 5858) of birds, of which 40% (n = 6) are regarded as species of international conservation importance. Our models highlighted that the strongest driver explaining variation in abundance and richness across sites was the type of buoy and the associated cultivation method applied. The older and fast-declining double headrope design, offered greater stability for birds to rest. Conversely, the newer and mechanizable single headrope design dominant method in our study site and projected to replace the older system, was unsuitable for birds. Our findings confirm the function of mussel farms as a sort of marine protected area where low anthropogenic disturbance, higher prey availability and suitable artificial structures promote the establishment of seabird communities with minimal impacts on harvest. However, we suggest that potential modernization of farming methods, important to meet future human demand, needs to be carefully assessed and compensated for, particularly where long-established seabird communities have formed in response to such practices.

The influence of the freshwater runoff on marine prokaryotes has been largelly studied in the pelagic environment, little is known about the effects on the prokaryotes in coastal sediments. We investigated the distribution of benthic prokaryotes in the northern Adriatic Sea, when an extreme Po River flood event determined high heterogeneity along the estuarine salinity gradient (from mainly freshwater to marine). The microbial diversity was assessed by 16S rRNA gene Illumina sequencing, the quantification of the dominant taxa of Bacteria and Archaea by microscopy techniques (CARD-FISH). Our results showed dominance of Bacteria (eight-fold higher) over Archaea, and highlighted Proteobacteria as the most represented phylum, followed by Bacteroidetes. Prokaryotic abundance, quantified by DAPI staining, was mainly affected by sediment characteristics (Total Organic C and Total N contents, and silt fraction). Abundance reached the highest values in sites directly affected by the plume (range 7.3 × 108 - 2.8 × 109 cell g−1). A considerable difference in prokaryotes composition was observed along the salinity gradient, with an increasing presence of freshwater taxa at stations more influenced by the river discharge. CARD-FISH analyses corroborated these findings, showing higher abundance of beta-Proteobacteria and Planctomycetes at stations closest to the river mouths. Nevertheless, a core microbiome (about 10% of the total OTUs) was present across all the study areas, indicating the ability of this assemblage to survive in rather diverse environmental conditions, differently impacted by the river plume. Our results show that the river plume can affect the diversity and distribution patterns of benthic prokaryotes far into the pro-delta, although further investigations are needed in order to understand how the mixing of bacterial communities of different origin might reflect on ecosystem functioning.

The Mar Piccolo is a semi-enclosed basin subject to different natural and anthropogenic stressors. In order to better understand plankton dynamics and preferential carbon pathways within the planktonic trophic web, an integrated approach was adopted for the first time by examining all trophic levels (virioplankton, the heterotrophic and phototrophic fractions of pico-, nano- and microplankton, as well as mesozooplankton). Plankton abundance and biomass were investigated during four surveys in the period 2013–2014. Beside unveiling the dynamics of different plankton groups in the Mar Piccolo, the study revealed that high portion of the plankton carbon (C) pool was constituted by small-sized (

Knowledge on ecosystem functioning can largely contribute to promote ecosystem-based management and its application. The Mar Piccolo of Taranto is a densely populated area at a high risk of environmental crisis. Here, planktonic primary production (PP) and heterotrophic prokaryotic production (HPP) were measured as proxies of functioning in three sampling sites located in two inlets at different levels of industrial contamination, during three sampling surveys (June 2013, February and April 2014). To have a better overall view and provide some insights into the benthic-pelagic coupling, we integrated PP and HPP in the water column with those in the sediments and then discussed this with the origin of the organic matter pools based on analysis of stable isotopes. Heavy metals and polychlorobiphenyls (PCBs) were also analysed in the surface (1 cm) sediment layer and related to the overall ecosystem functioning. Multidimensional scaling (MDS) analysis, based on the main data, clearly separated the second inlet from the first one, more severely impacted by anthropogenic activities. The stable isotope mixing model suggested the prevalent terrestrial/riverine origin of the particulate organic matter pools (mean 45.5 %) in all sampling periods, whereas phytoplankton contributed up to 29 % in February. Planktonic PP and HPP rates followed the same pattern over the entire study period and seemed to respond to phytoplankton dynamics confirming this community as the main driver for the C cycling in the water column. On the contrary, benthic PP rates were almost negligible while HPP rates were lower or comparable to those in the water column indicating that although the Mar Piccolo is very shallow, the water column is much more productive than the surface sediments. The sediment resuspension is likely responsible for a pulsed input of contaminants into the water column. However, their interference with the proper functioning of the pelagic ecosystem seems to be limited to the bottom layers. © 2015, Springer-Verlag Berlin Heidelberg.

Notwithstanding the increasing amount of researches on the effect of ocean acidification (OA) on marine ecosystems, no consent has emerged on its consequences on many prokaryote-mediated processes. Two mesocosm experiments were performed in coastal Mediterranean areas with different trophic status: the summer oligotrophic Bay of Calvi (BC, Corsica, France) and the winter mesotrophic Bay of Villefranche (BV, France). During these experiments, nine enclosures (∼54 m 3 ) were deployed: 3 unamended controls and 6 elevated CO 2 , following a gradient up to 1250 μatm. We present results involving free-living viral and prokaryotic standing stocks, bacterial carbon production, abundance of highly active cells (CTC+), and degradation processes (beta-glucosidase, chitinase, leucine-aminopeptidase, lipase and alkaline phosphatase activities). The experiments revealed clear differences in the response of the two prokaryotic communities to CO 2 manipulation. Only abundances of heterotrophic prokaryotes, viruses and lipase activity were not affected by CO 2 manipulation at both locations. On the contrary, the percent of CTC+ was positively correlated to CO 2 only in BC, concomitantly to a bulk reduction of [ 3 H]-leucine uptake. The other tested parameters showed a different response at the two sites suggesting that the trophic regime of the systems plays a fundamental role on the effect of OA on prokaryotes through indirect modifications of the available substrate. Modified degradation rates may affect considerably the export of organic matter to the seafloor and thus ecosystem functioning within the water column. Our results highlight the need to further analyse the consequences of OA in oligotrophic ecosystems with particular focus on dissolved organic matter.

To understand to what extent depositional dynamics and riverine input contribute to shape the microbial benthic community structure in coastal systems, surface sediments were collected along one nearshore and two land-sea transects in the Po River prodelta, and analyzed for lithology, sediment structures, grain-size, short-lived radioisotopes (7Be and 137Cs) and organic matter (OM) quantity and origin (C, N, stable isotopes). The most recent surface supply (i.e. 5–6 mo = SUP layer) and the underneath, older sub-surface deposits (i.e. >6 mo = SUB layer) were analyzed at six selected sampling sites and checked for possible differences in the microbial community abundance and structure. According to different depositional dynamics, three distinct groups of sites were detected: nearshore muddy and sandy sites, and offshore sites. Sedimentary records reflected the interplay of different elements and/or processes acting in this complex and highly dynamic system. River-derived sediments, as depicted by high contribution of silty particles and recent riverine OM inputs, were confined to nearshore locations in front of the main river mouth. They resulted highly correlated to bacterial distribution and prokaryotic abundances in SUP layer. Nevertheless, in subsurface sediments affected by the delivery of high amount of mud, potential burial phenomena and/or the development of anoxic conditions occurred, leading to a change in the bacterial community structure. We speculated that the decrease of Gamma- and increase of Delta-Proteobacteria in the SUB layer could be related to their sulfur-oxidizing and sulfate-reducing activities, respectively. On the other hand, at offshore sites, the presence of a low, and regular sedimentary input and less intense hydrodynamic conditions favored a more stable microbial structure across surface and subsurface sediments. Four discriminating proxies, such as grain-size representing the system energy, Total N as an indicator of land-derived nutrient inputs, 7Be as a tracer of the freshness of riverine discharge, and stable C isotope as an indicator of the type and age of OM, mainly summarize the complex relationships between sedimentary dynamics and bacterial community structure in the Po River prodelta area.

From July 2010 to July 2012, free-living nematodes were investigated in terms of abundance, genera and trophic composition at the long term St. C1 (depth 18 m), located in the Gulf of Trieste (northern Adriatic Sea). The integration of these results with environmental (e.g. sediment grain-size, Biopolymeric C and Chl a) and biological variables (benthic diatom biomass and composition) collected synoptically with nematodes, allowed to clarify the linkage between these organisms and another ecosystem component, i.e. benthic diatoms. The observed peaks of nematode abundance in summer samplings were ascribable almost exclusively to piercing nematodes that feed on microalgae (Chromadoridae and, among them, Ptycholaimellus) and were concomitant with the highest numbers of benthic diatoms. DISTLM outputs further corroborated this interaction by indicating Chl a, i.e. a proxy of benthic diatoms, as the only environmental variable that significantly shaped nematode assemblage over the 2-year period. This linkage was not explained only quantitatively (i.e. more diatoms supported more nematodes) but also qualitatively. During winter, in fact, the presence of heavily silicified diatoms co-occurred with nematode minima and the lowest percentage of piercing organisms, suggesting an overall minor ability of the assemblage in using this feeding strategy. In a benthic ecosystem functioning point of view, the observed seasonal pattern of variation in both nematodes and benthic diatoms suggests that more of the energy flowing to nematodes during the summer derives directly from benthic diatom primary production while in the winter this linkage is less important.

The subcellular effects of pollution were evaluated using two lysosomal biomarkers in mussels, Mytilus galloprovincialis, deployed periodically over a period of 5 years in a harbour area in the Bay of Muggia (Gulf of Trieste, North Adriatic Sea) that is strongly influenced by anthropogenic activities. Mussels were collected from a clean marine farm and analysed (sample T0). A sub-sample was transplanted to the harbour site (sample M) and analysed after about 12 weeks. An additional sub-sample was relocated within the farm as a control and was also tested at the end of the 12-week period (sample T1). The transplantation procedures were repeated twice yearly for 5 consecutive years, starting in 2009. Two well-established lysosomal biomarkers, i.e. lysosomal membrane stability and lipofuscin accumulation, were evaluated in hepatopancreas cells. The body condition index and mortality rate were also assessed. Moreover, various pollutants were determined in both mussel flesh, for a better comprehension of the biological response, and sediments, for a general characterization of the study area. As a whole, the applied biomarkers were found to be appropriate for determining the responses of mussels to environmental pollutant loads over time. Variations in lysosomal membrane stability and lipofuscin content were mostly related to total PAHs and metals respectively. Our results confirm the usefulness of active biomonitoring in evaluating pollution trends in marine coastal areas and in particular the value of lysosomal biomarkers as a rapid screening tool for highlighting pollutant effects at least at organism level.

Gas hydrothermal vents are used as a natural analogue for studying the effects of CO2 leakage from hypothetical shallow marine storage sites on benthic and pelagic systems. This study investigated the interrelationships between planktonic prokaryotes and viruses in the Panarea Islands hydrothermal system (southern Tyrrhenian Sea, Italy), especially their abundance, distribution and diversity. No difference in prokaryotic abundance was shown between high-CO2 and control sites. The community structure displayed differences between fumarolic field and the control, and between surface and bottom waters, the latter likely due to the presence of different water masses. Bacterial assemblages were qualitatively dominated by chemo- and photoautotrophic organisms, able to utilise both CO2 and H2S for their metabolic requirements. From significantly lower virioplankton abundance in the proximity of the exhalative area together with particularly low Virus-to-Prokaryotes Ratio, we inferred a reduced impact on prokaryotic abundance and proliferation. Even if the fate of viruses in this particular condition remains still unknown, we consider that lower viral abundance could reflect in enhancing the energy flow to higher trophic levels, thus largely influencing the overall functioning of the system.

The Mar Piccolo of Taranto, classified as a ‘Site of National Interest’ (SIN), is a semi-enclosed basin divided into two inlets with lagoon features and sea influences, seriously affected by anthropic activities. In the framework of the RITMARE project, a study has been carried out to evaluate the functionality of this ecosystem. As part of this work, measurements of the water abiotic parameters were performed in order to assess the physical–chemical features of this area after the activation, in the last decade, of treatment plants for various urban and industrial dumping. Seawater intrusions and continental inputs, as well as several submarine freshwater springs, clearly affect physical–chemical characteristics of the water column in the two inlets. This finding suggests that small-scale patterns in water circulation have the potential to influence the chemical properties of the seawater. The comparison with a 20-year dataset reveals a drastic decrease in nutrient concentrations after the year 2000, validating the functionality of the treatment plants. The reduction of nutrient inputs into the basin (up to −90 % in the first inlet characterized by lower hydraulic residence time) has changed the biogeochemical characteristics of the Mar Piccolo from being relatively eutrophic to moderately oligotrophic.

The EU Marine Strategy Framework Directive 2008/56/EC (MSFD) defines a framework for Community actions in the field of marine environmental policy in order to achieve and/or maintain the Good Environmental Status (GES) of the European seas by 2020. Microbial assemblages (from viruses to microbial-sized metazoa) provide a major contribution to global biodiversity and play a crucial role in the functioning of marine ecosystems, but are largely ignored by the MSFD. Prokaryotes are only seen as "microbial pathogens", without defining their role in GES indicators. However, structural or functional prokaryotic variables (abundance, biodiversity and metabolism) can be easily incorporated into several MSFD Descriptors (i.e. D1. Biodiversity, D4. Food webs, D5. Eutrophication, D8. Contaminants and D9. Contaminants in seafood) with beneficial effects. The present review provides a critical analysis of the current MSFD descriptors and illustrates the reliability and advantages of the potential incorporation of some prokaryotic variables within the set of indicators of marine environmental quality. Following a cost/benefit analysis against scientific and economic criteria, we conclude that marine microbial components, and particularly prokaryotes, are highly effective for detecting the effects of anthropogenic pressures on marine environments and for assessing changes in the environmental health status. We thus recommend the inclusion of these components in future implementations of the MSFD.

During the 2006 Italian Antarctic expedition a diel sampling was performed close to Cape Hallett (Ross Sea) during the Austral summer. Under-ice seawater samples (∼4 m) were collected every 2 h for 28 h in order to estimate prokaryotic processes' variability and community structure dynamics. Prokaryotic and viral abundances, exoenzymatic activities (β-glucosidase, chitinase, lipase, alkaline phosphatase and leucine aminopeptidase), prokaryotic carbon production ( 3 H -leucine incorporation) and community structure (Denaturing Gradient Gel Electrophoresis – DGGE fingerprints) were analysed. Results showed that the diel variability of the prokaryotic activity followed a variation in salinity, probably as a consequence of the periodical thawing of sea ice (driven by solar radiation and air temperature cycles), while negligible variation in viral and prokaryotic abundances occurred. The Bacterial and Archaeal community structures underwent an Operational Taxonomic Units (OTUs) temporal shift from the beginning to the end of the sampling, while Flavobacteria -specific primers highlighted high variations in this group possibly related to sea ice melting and substrate release.