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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. This 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. Thus, we recommend the inclusion of these components in future implementations of the MSFD.

Ammonium-oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan-Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep-sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2-fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]-bicarbonate incorporation experiments combined with shotgun [14C]-proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto- and heterotrophic ABD. In some deep-sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.

Meso- and bathypelagic ecosystems represent the most common marine ecological niche on Earth and contain complex communities of microorganisms that are for the most part ecophysiologically poorly characterized. Gradients of physico-chemical factors (for example, depth-related gradients of light, temperature, salinity, nutrients and pressure) constitute major forces shaping ecosystems at activity 'hot spots' on the ocean floor, such as hydrothermal vents, cold seepages and mud volcanoes and hypersaline lakes, though the relationships between community composition, activities and environmental parameters remain largely elusive. We report here results of a detailed study of primary producing microbial communities in the deep Eastern Mediterranean Sea. The brine column of the deep anoxic hypersaline brine lake, L'Atalante, the overlying water column and the brine-seawater interface, were characterized physico- and geochemically, and microbiologically, in terms of their microbial community compositions, functional gene distributions and [(14)C]bicarbonate assimilation activities. The depth distribution of genes encoding the crenarchaeal ammonia monooxygenase alpha subunit (amoA), and the bacterial ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (RuBisCO), was found to coincide with two different types of chemoautotrophy. Meso- and bathypelagic microbial communities were enriched in ammonia-oxidizing Crenarchaeota, whereas the autotrophic community at the oxic/anoxic interface of L'Atalante lake was dominated by Epsilonproteobacteria and sulfur-oxidizing Gammaproteobacteria. These autotrophic microbes are thus the basis of the food webs populating these deep-sea ecosystems.

The optical properties of the waters of five different stations, three located in the Messina Strait and two near the Strait (open sea), were analysed. Direct spectral measurements of the downward solar irradiance (290 - 800 nm) at different depths (0.5 m, 7 m, 10 m, 13 m, 20 m) were made using a cosine sensor connected to a spectroradiometer. Water samples were collected in the surface layer and their absorption spectra were analysed. The natural fluorescence profiles, along the water column, were determined using a fluorometer (SBE 911plus - Sea Teach). The spectral attenuation coefficient (K(lambda)), the variation of K(lambda) in different wavelength ranges (deltaK(deltalambda)), the wavelength corresponding to minimum value of K(lambda), the spectral depths of penetration of both 1% and 10% of the sub-surface irradiance values (P(lambda)), the depths of 1% of penetration of UVB, UVA and PAR, the depth ranges of the maxim concentration of Chl a and superficial CDOM were measured at each station. The maximum solar UVB penetration was about 65% of the photic zone and the maximum UVA penetration was nearly 100% (data of the Ionic sea station). Thus, a large part of the photic zone was exposed to UV radiation sufficient to cause a possible reduction in the photosynthetic activity of phytoplankton. The spectral penetration of solar radiation, especially UVB radiation, was significantly different in the three stations of the Strait with respect to the two stations studied in the open sea. This shows that variations in the spectral attenuation along the water column can be used as an indicator of properties of the water body.

Phytoplankton size is a significant functional trait affecting many ecological processes and influencing the carbon fate and the trophic regimes of the ecosystems. In this study, we examined the effect of the lateral advection of nutrient-rich Messina Mixed Waters on the phytoplankton size structure and community composition in the euphotic layer of the Gulf of Augusta (Western Ionian Sea) in early autumn. The chlorophyll a concentration ranged from 0.08 to 0.8 mg m−3 and the phytoplankton abundances ranged from 21 × 103 to 245 × 103 cells L−1. The size structure of phytoplankton biomass, obtained by sequential filtration of water samples, suggested the dominance of micro-planktonic diatoms in an active Deep Chlorophyll Maximum (DCM) whereas smaller forms were mainly represented by phytoflagellates. A short-term tidal-induced variability of the assemblage structure was observed at a "sentinel" station located at the Gulf shelf-break where lateral advection due to meso-scale dynamics sustained most of the phytoplankton biomass. Our research shows that, in stratified conditions, nutrient enrichment by lateral advection at DCM modifies the size-structure of phytoplankton with respect to that expected from the reference baseline oceanic model validated in open ocean waters. In particular, while smaller fraction incidences reveal a surface oligotrophic system, an increase of the micro-sized fraction is triggered at DCM: this indicates the prevalence of "new production" processes which is a quite unusual condition for the Mediterranean DCM in early autumn, when trophic web is typically sustained by "regenerate production". Our observations suggest that both "microbial" and "herbivore" pathways could coexist and regulate the carbon flow in the Gulf in this season. • Lateral advection of nutrient-rich waters shaped local phytoplankton size-structure. • Micro-phytoplankton fraction incidence overcomes the reference baseline oceanic model. • A micro-sized diatoms core pool dominated spatial and time-series coastal assemblages. • Meso-scale dynamics influenced phytoplankton composition and relative size incidences. [ABSTRACT FROM AUTHOR]