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Abstract The water quality of Sicilian transitional and coastal marine areas was investigated by evaluating the distribution of Enterococcus spp.; as a reference, two sewage samples were also analysed. The epidemiological implications of their presence were considered. Enterococcal strains isolated by culture methods were phenotypically and molecularly identified and their susceptibility to antibiotics tested. High phenotypic variability was detected, with low specific identification for 46% of the isolated strains. E. casseliflavus , isolated from transitional environments only, predominated; in coastal and sewage waters E. faecium prevailed, occurring also in transitional environments, where multiple antibiotic resistances were found. Ampicillin and vancomycin resistant enterococci were isolated exclusively from transitional environments. The dynamics of dissemination of antibiotic resistant enterococci in aquatic environments located across the South-North migration route of many wild birds could be very complex, emphasising the relevance of epidemiological studies on transitional aquatic environments as reservoirs of pathogenic enterococci, as well as on sedentary seagulls and migratory wild birds as carriers and spreaders of antibiotic resistant enterococci. [ABSTRACT FROM AUTHOR]

Abstract: Phytoplankton community size drives the rates of biogenic carbon and the overall structure and dynamics of the marine pelagic food web. The Straits of Magellan, an inland passage between the Pacific and Atlantic Oceans, can be separated into three main sub-basins: the western-Pacific, the V-shaped central zone, and the eastern-Atlantic. To provide insights into the food structure of the phytoplankton community, size-fractionated chlorophyll a concentration and primary production rates were measured across the three sectors of the Magellan Straits in four periods between 1989 and 1995 in the Straits. Phytoplanktonic biomass and production ratios provided ecological insights into the food web structure, including the relevance of grazing in its largest fraction. The micro-phytoplanktonic fraction (>10μm) in the Pacific sub-basin is significantly less abundant than in the Central and Atlantic ones. Conversely, the lowest abundance of the pico-fraction (<2.0μm) is encountered in the Atlantic sub-basin. The observed patterns agree with the diffusion of smaller-size fractions from the western towards the easternmost sector of the Straits, and suggest that the largest phytoplankton tend to accumulate in the inner stretch of the Straits, being constrained by a clockwise gyre generated by tidal phases or partially spilling out into the Atlantic sector. The most active grazing activities occur in the Central sub-basin during the spring bloom and appear even stronger in summer. Our results pinpoint also that the basic levels of the planktonic food web rely on the nanophytoplankton (10–2μm) fraction, which is the main contributor to the continuum multivorous food web. When external energy (e.g. nutrient pulses from land freshwater and water mixing) enters the system, the structure of the plankton in the Straits shifts towards the herbivorous food web and is characterized by the presence of large-size diatoms. This dynamics keeps the system in a persistent mesotrophic state, featuring a lower trophic status than the Antarctic ones but much higher than that of oligotrophic temperate areas. [Copyright &y& Elsevier]

Abstract: In the frame of a multidisciplinary international joint effort, supported by CIESM, phytoplankton composition, distribution and activity in summer and late autumn in the Southern Tyrrhenian Sea were investigated. The main aim of the study was to obtain a preliminary characterization of the autotrophic community structure of a poorly investigated and complex basin during two contrasting seasonal conditions (stratification vs homogeneity). On both occasions the phytoplankton biomass, as chlorophyll a, was low in the euphotic layer of water column (8.9mgm−2 in July and 10.7mgm−2 in December), with a clear dominance of the pico-phytoplanktonic component (64% and 76%, respectively), and a pronounced summer Deep Chlorophyll Maximum. Interestingly, primary production was higher in December (429mgCm−2 d−1) than July (273mgCm−2 d−1), again with a major contribution of pico-class in both seasons (90% and 52% in late autumn and summer, respectively). The dominant contribution of small size classes to the total photosynthetic efficiency and their fast carbon turnover time within the community hint at a preferential carbon pathway through the small-sized components of the food web that contrasts with the traditional views of the Tyrrhenian Sea as a typical component of the temperate Western Mediterranean Sea. [Copyright &y& Elsevier]

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. [ABSTRACT FROM AUTHOR]

Planktonic communities hold a relevant role within the EU Marine Strategy Framework Directive (MSFD). In view of reaching the Good Environmental Status of marine ecosystems, within this Directive the phyto- and zooplanktonic communities have received great attention, while Prokaryotes (Bacteria, Archaea, and Cyanobacteria) have been neglected. Indeed, the relevance of microbes (particularly of the faecal pollution indicators) as water quality indicators, the role that microorganisms play within the biogeochemical fluxes and in the whole ecosystem functioning, are all important features that deserve to be focused within the MSFD. The present study aims at reviewing the main issues where prokaryotic variables find useful application as descriptors of environmental status, trying to develop a panel of prokaryotic indicators suitable for the environmental quality assessment. From a survey of scientific literature and on field datasets, prokaryotic abundance and activities (enzymatic hydrolysis, prokaryotic production, and respiratory rates) are here chosen as early warning sentinels to detect changes in environmental quality, using an integrated approach with trophic (chlorophyll-a, particulate and dissolved organic matter) measurements. [ABSTRACT FROM AUTHOR]

Ammonium-oxidizing chemoautotrophic members of T haumarchaea 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 G ammaproteobacteria with virtually no T haumarchaea 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 A lteromonas 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. [ABSTRACT FROM AUTHOR]

Abstract: The response of both microbial activities and prokaryotic abundances to environmental variability was studied in a transitional Mediterranean system (Oliveri–Tindari, Italy) during two yearly surveys (1997–'98 and 2005–'06). The total enzymatic (leucine aminopeptidase, β-glucosidase, alkaline phosphatase) and respiratory activity rates as well as of the abundances of total prokaryotes, culturable heterotrophic bacteria, faecal coliforms and enterococci were measured in surface waters of four brackish ponds, together with temperature, salinity, dissolved oxygen, pH, inorganic nutrients, chlorophyll-a and particulate organic carbon and particulate nitrogen determinations. The seasonal and interannual patterns of microbial parameters were investigated in relation to environmental variations. Both the microbial activities and the abundances of culturable heterotrophic bacteria, faecal coliforms and enterococci varied significantly among the ponds, reflecting their haline and trophic variability. Significant seasonal and interannual variations were found in the patterns of microbial activity, but not in total prokaryotic abundance, in response to temperature, dissolved oxygen and trophic changes. Microbial parameters showed a different response to environmental variability in the two examined periods: during 1997–'98, increases in the microbial activity rates and culturable bacterial counts were positively related with the trophic changes, while during 2005–'06 the patterns of leucine aminopeptidase, alkaline phosphatase and respiratory activities and of total prokaryotic and culturable bacteria abundances were uncoupled with those of temperature, salinity, dissolved oxygen, particulate organic carbon and chlorophyll-a. Changes in the relative importance of environmental and trophic variables between the two considered periods explain this discrepancy. [Copyright &y& Elsevier]

The distribution of the prokaryotic biomass (from both abundance and cell volume measurements) and microbial community respiration (by ETS activity) in the main water masses of the Southern Tyrrhenian Sea were studied. The data were collected from surface to the bottom depth (max 3600 m) in July and December 2005. Prokaryotic abundance and microbial respiration were higher in summer than late-autumn and decreased with depth in accordance with the water masses. The opposite was found for the prokaryotic cell volumes that increased with depth and were higher in December. The cell carbon content varied within the water masses and study periods (range 9-34 fg C cell-1) and overestimations and underestimations of biomass there would have been by using the routinely adopted conversion factor (20 fg C cell-1). The depth-integrated respiratory rates resulted comparable in the photic and aphotic layers. In July, 210 and 225 mg C m-2 day-1 in the euphotic and aphotic zones, respectively, were remineralized while in December, 112 and 134 mg C m-2 day-1, respectively, were. Speculations to quantify the carbon flow mediated by microbial community suggested the occurrence of different microbial behavior within the different water masses. [ABSTRACT FROM AUTHOR]

In the past two decades, optical properties of chromophoric dissolved organic matter (CDOM) in marine environments have been extensively studied. Many of these studies report CDOM properties for the offshore environment where this complex mixture of optically active compounds is strongly diluted. Nevertheless, autochthonous and allochthonous sources have been identified and sinks related to photodegradation and bacterial activity have been demonstrated. The calculation of the spectral slope of the CDOM absorption curve has been proven to be useful and is often reported. However, a rigorous uncertainty analysis of the slope calculation is rarely reported. In this paper, we propose a method to evaluate the uncertainty of CDOM spectral slope calculated between 270 and 400 nm, using both naturally sampled and artificial solutions. We use these results to study the ultra-oligotrophic waters of the Mediterranean Sea (central eastern basin), where little is known about CDOM spatial distribution. We show that dilutions of both artificial and natural samples produce a Gaussian distribution of spectral slopes, indicating that consistent values may be determined, with a typical uncertainty of ±0.0004 nm when absorption at 300 nm was greater then 0.1 m (0.1 m pathlength). Comparing the distribution of spectral slopes from central eastern basin samples to a Gaussian distribution, we show differences between measurements that were significantly different. These values allow us to distinguish possible sources (algal derived CDOM), sinks (e.g. photo-bleaching) at different depths. We propose a subdivision of CDOM compounds into refractory and semilabile/refractory pools and evaluate the CDOM spectral slope of algal derived CDOM released at or near deep chlorophyll maximum. [ABSTRACT FROM AUTHOR]

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 [14C]bicarbonate assimilation activities. The depth distribution of genes encoding the crenarchaeal ammonia monooxygenase α 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 ISME Journal (2007) 1, 743–755; doi:10.1038/ismej.2007.83; published online 4 October 2007 [ABSTRACT FROM AUTHOR]

Abstract: This paper concerns the current debate as to whether oceans are heterotrophic or autotrophic environments. Microbes are responsible for the assimilation and remineralization of CO2 in the sea and microbial processes are involved in the Earth climatic change. The variability of microbial biomass and activities were studied in the Mediterranean Sea which represents a suitable basin for mapping the trophic regimes by the study of biogeochemical processes. The surveys were carried out in the epi-, meso- and bathy-pelagic zones of the Central Mediterranean Sea from 1996 to 2002. Bacterial abundance, leucine aminopeptidase (LAP) and β-glucosidase (β-GLU) activities, bacterial carbon production (BCP), community respiration (R) and primary production (PP) were the main parameters investigated. Biomass and activities seasonally varied in epipelagic and, to some extent, in meso- and bathy-pelagic layers too and several trophic ratios were determined, showing different scenarios in the different areas and seasons. In the euphotic layer, bacterial growth efficiency (BGE) widely ranged between 4% and 50% showing a decreasing trend from estuaries towards pelagic areas in alignment with the trophic gradient from the Northern Adriatic to the Ionian Sea. However, BGE did not correlate to PP and temperature. The Central Mediterranean Sea showed different trophic regimes in the examined areas and seasons. In the Northern Adriatic Sea in winter, the trophic balance appeared to move towards autotrophy and a positive C budget resulted. An opposite scenario happened in summer when the trophic balance moved to heterotrophy and a negative C budget occurred. In the Ionian Sea, the overall balance turned always towards remineralization. However, on annual time scale, the Central Mediterranean Sea seems to show a tendency towards a heterotrophic system. [Copyright &y& Elsevier]

Marine primary production (PP) is a key factor in the regulation of the global carbon cycle, with important potential feedback on climate. Seventy percent of marine PP is generated by phytoplankton photosynthesis. However, the phytoplankton productivity rate is dependent on the photo-physiological state of phytoplankton cells, as well as other environmental conditions. To consider these variables appropriately, refine the current estimates of PP, and reduce the laboursome and lengthy methodologies of radiocarbon estimates, we have created "Phyto-VFP" (Variable Fluorescence Phytoplankton Production), a new bio-optical model classified as a Wavelength and Depth-resolved (WDR) model. The model integrates the effect of the photo-acclimation processes on the "active" fraction of the phytoplankton population with the dynamic of the water column, parametrised through a series of laboratory experiments based on in vivo variable fluorescence measures on the marine diatom Skeletonema costatum (Greville) Cleve. The performance of Phyto-VFP was compared with concurrent estimates of radiocarbon (14C) uptakes, under different dynamic and optical conditions, during two oceanographic cruises (SAMCA3 and SAMCA4) in the Mediterranean Sea. The low Root Mean Square Differences (RMSDs) show that Phyto-VFP performs well when estimating phytoplankton PP. When compared to other bio-optical models, Phyto-VFP estimates of PP in coastal waters were closer to radiocarbon measurements than other models could predict [ e.g. , the Morel model (MM)]. The application of Phyto-VFP to the SAMCA dataset and its comparison to MM allowed the assessment of model performance under three different physical and biological conditions, in which it was possible to analyse how photo-physiological responses of phytoplankton influence PP. • Phyto-VFP estimates phytoplankton Primary Production using variable fluorescence. • Phyto-VFP combines phytoplankton physiological processes with water column dynamics. • The model attained a performance similar to the most widely Primary Production models. • Phyto-VFP shows a higher predictive skill than Morel model in coastal waters. [ABSTRACT FROM AUTHOR]