Cesare Corselli

Comparison of Different Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Complex Bacterial Communities

ABSTRACT ITSF and ITSReub, constituting a new primer set designed for the amplification of the 16S-23S rRNA intergenic transcribed spacers, have been compared with primer sets consisting of 1406F and 23Sr (M. M. Fisher and E. W. Triplett, Appl. Environ. Microbiol. 65:4630-4636, 1999) and S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 (L. Ranjard et al., Appl. Environ. Microbiol. 67:4479-4487, 2001), previously proposed for automated ribosomal intergenic spacer analysis (ARISA) of complex bacterial communities. An agricultural soil and a polluted soil, maize silage, goat milk, a small marble sample from the façade of the Certosa of Pavia (Pavia, Italy), and brine from a deep hypersaline anoxic basin in the Mediterranean Sea were analyzed with the three primer sets. The number of peaks in the ARISA profiles, the range of peak size (width of the profile), and the reproducibility of results were used as indices to evaluate the efficiency of the three primer sets. The overall data showed that ITSF and ITSReub generated the most informative (in term of peak number) and reproducible profiles and yielded a wider range of spacer sizes (134 to 1,387) than the other primer sets, which were limited in detecting long fragments. The minimum amount of DNA template and sensitivity in detection of minor DNA populations were evaluated with artificial mixtures of defined bacterial species. ITSF and ITSReub amplified all the bacteria at DNA template concentrations from 280 to 0.14 ng μl−1, while the other primer sets failed to detect the spacers of one or more bacterial strains. Although the primer set consisting of ITSF and ITSReub and that of S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 showed similar sensitivities for the DNA of Allorhizobium undicula mixed with the DNA of other species, the S-D-Bact-1522-b-S-20 and L-D-Bact-132-a-A-18 primer set failed to detect the DNA of Pseudomonas stutzeri.

Present-day coccolith fluxes recorded in central eastern Mediterranean sediment traps and surface sediments

Two sediment traps were deployed in time series collection from November 1991 to August 1994 at 3000 and 3500 m, respectively, above and below the oxygenated sea water/anoxic brine interface in the Bannock Basin, central eastern Mediterranean. Here, the coccolithophore flux and its contribution to the carbonate particulate flux are presented for the 3000 m trap and compared with the record in eastern Mediterranean surface sediments. A marked seasonal variation is observed in the fluxes of total mass, total coccoliths and whole coccospheres, with flux maxima in late winter and spring. The annual coccolith flux of 1×1010 coccoliths m?2 year?1 measured in the deep waters of Bannock Basin is much lower than published data from most other oceanographic settings, even when corrected for the trap efficiency of ~23% calculated from the 230Th flux. The biogenic and lithogenic fluxes are primarily controlled by coccolithophore production and Saharan dust input, respectively. The calculated coccolith and coccosphere settling rates, estimated from the comparison of maximum pigment concentration in the surface ocean and arrival of maximum flux at 3000 m water depth, ranged from 17 to 25 m day?1 for coccoliths and 100 m day?1 for coccospheres. At the study site, carbonate dissolution is a minor process at both the trap depth and at the sea floor in both oxic and anoxic conditions, and there is a high preservation of coccolith CaCO3. Coccolithophores are the main contributor to the biogenic carbonate flux, followed by thoracosphaerids. Emiliania huxleyi and Florisphaera profunda followed by Syracosphaera, Helicosphaera carteri and Calcidiscus leptoporus are the dominant species in the sediment trap and surface sediments.

Recent terrestrial and carbonate fluxes in the pelagic eastern Mediterranean: a comparison between sediment trap and surface sediment

A sediment trap mooring was deployed in the central eastern Mediterranean from November 1991 to August 1994. At 3000 m water depth, total mass, Al, Ca, Mg, Sr and 230Th fluxes recovered by the sediment trap are highly seasonal, with highest fluxes during early spring in 1992 and 1993, and during late-spring/early-summer in 1994. Comparison of historic annual satellite-derived chlorophyll records (coastal zone colour scanner) with the trap flux time series indicates a lag of 4–6 months between maximum primary production in the surface ocean and maximum flux recorded by the trap. Only the flux of coccospheres to the trap is at a maximum ~1 month after maximum pigment concentrations in surface waters, a value commonly found in other areas. Quantification of the inorganic (lithogenic) flux to the trap indicates that Saharan dust is likely to be the major contributor to the trap mass flux. The trapping efficiency of the sediment trap, as calculated from the intercepted 230Th flux, is only 23%, and the trap Al-flux is similarly ×4 lower than Al fluxes measured in nearby uppermost sediments. Compared with surface sediments, the trap-intercepted carbonate fluxes are even lower (×9) than the corresponding lithogenic fluxes. This is partly due to the very low abundance of large (>32 m) foraminifera and pteropods found in the trap material compared to the surface sediment. We speculate that the period of our sediment trap deployment was insufficiently long to recover episodical large fluxes, such as may be triggered by North Atlantic Oscillation variations.

First evidence of benthic communities based on chemosynthesis on the Napoli mud volcano (Eastern Mediterranean)

Abstract Some molluscan valves attributed to Myrtea sp. (Lucinidae), Vesicomya sp. and another undetermined Vesicomydae were sampled in 1993 (cruise TTR3/Leg2) and 1994 (cruise UM94) by coring on the top of the Napoli Dome, a mud volcano located on the Mediterranean Ridge, at about 1900 m of water depth. These bivalves belong to an unknown, apparently rich benthic community associated to the sulphides and methane-rich emissions that characterize the Napoli Dome. Outside the Mediterranean, deep-sea Lucinidae and Vesicomyidae are associated with cold-seeps and hydrothermal vents and are known to be sustained by bacterial chemosynthetic activity based on sulphide and/or methane oxidation. The same explanation is given for this newly discovered deep Mediterranean fauna, firstly described here.

SULPHATE-RELATED EQUILIBRIA IN THE HYPERSALINE BRINES OF THE TYRO AND BANNOCK BASINS, EASTERN MEDITERRANEAN

Abstract The Tyro and Bannock Basins, which are depressions in the eastern Mediterranean, contain hypersaline anoxic brines. These brines are of different composition: Tyro brine is primarily an early-stage halite (NaCl) brine, whereas Bannock brine includes the more soluble ions of late-stage evaporite minerals. Accordingly, the Bannock brine contains a much greater sulphate concentration than the Tyro Brine. This difference in sulphate concentration is reflected in the concentrations of ions such as Ca, Sr and Ba, which form sparingly soluble sulphate minerals. Equilibrium calculations using the Pitzer specific ion interaction model indicate that the brines in both basins are saturated with respect to gypsum (CaSO 4 -2H 2 O) and supersaturated to saturated with respect to dolomite (CaMg(CO 3 ) 2 ). The degree of saturation with respect to dolomite is greater in the Bannock Basin than it is in the Tyro Basin. Correspondingly, recent gypsum crystals and dolomite hardgrounds have been found in the Bannock Basin but not in the Tyro Basin. The Tyro brine is homogeneous in composition, whereas the Bannock brine demonstrates a clear two-layer brine structure. At the interface of the upper and the lower brine distinct positive anomalies occur in the total alkalinity and the concentration of phosphate, and negative anomalies occur in the concentrations of Mn 2+ and the rare earth elements (REE). These anomalies and the observed association of gypsum/dolomite in the sediments are all consistent with a recent precipitation of dolomite and gypsum in the Bannock Basin. The brines in both basins are also saturated with respect to barite (BaSO 4 ). The 87 Sr/ 86 Sr and δ 34 S ratios of the Bannock brines are amazingly consistent but differ dramatically from the values for modern or Messinian-age seawater. The Sr concentration and Sr and S isotope ratios in the gypsum crystals indicate that most of these crystals have resulted from precipitation/recrystallization from the brine and not from seawater. The observed variations between crystals are thought to reflect the recrystallization of (sub-) outcropping Messinian gypsum with a low 87 Sr/ 86 Sr ratio in the presence of seawater or brine fluids and with different extents of diagenesis.

Brine formation and gypsum precipitation in the Bannock Basin, Eastern Mediterranean

Abstract Sixty kilograms of gypsum crystals were collected at two dredging stations within a small anoxic, hypersaline basin, named the Bannock Basin, close to the Sirte Abyssal Plain. The basin was investigated in some detail by means of ten precision-positioned piston and gravity cores, one Nansen-bottle hydrocast and three CTD stations. The sediments of the basin floor are dark, H 2 S rich and commonly laminated, and contain centimetric crystals of gypsum. The water column above the basin has normal salinity down to a depth of 3150 m; below this depth the basin is filled with hypersaline brines, formed from the dissolution of Messinian evaporites, outcropping on the steep eastern wall. When the brines reach the necessary concentration in Ca and in SO 4 , gypsum may precipitate along the steep eastern wall and within the sediments on the basin floor. The very recent age of the gypsum is proved by the inclusions of Quaternary planktonic fauna (formainifera and pteropods) and by radiometric techniques.

Late Pleistocene–Holocene planktonic assemblages in three box-cores from the Mediterranean Ridge area (west–southwest of Crete): palaeoecological and palaeoceanographic reconstruction of sapropel S1 interval

Planktonic foraminiferal and calcareous nannofossil assemblages of three box-cores from the western–central part of the Mediterranean Ridge area were investigated and correlated. In particular we focused on the most significant faunal and floral signals recorded before, during and after sapropel S1 deposition. The interval preceding S1 is characterised by an increasing trend of the two planktonic foraminiferal species, Globorotalia inflata and Truncorotalia truncatulinoides, that are usually related to a well developed cold and deep mixed layer. This change is supported also by the rarity of warm water coccolithophorid species and by the presence of the deep dwelling species Florisphaera profunda. The beginning of S1 is marked by the disappearance of G. inflata and T. truncatulinoides and by the significant increase in abundance of Globigerinoides ruber, especially the rosea variety usually considered indicative of warmer conditions. Warm water species increase also within the coccolithophorid assemblage, while the upwelling species Reticulofenestra spp. suddenly decreases and remains low across the whole sapropel interval. The sedimentary expression of the end of anoxia is the upper boundary of the oxidised level observed above S1 in the three box-cores. Across this boundary we detect a small but well defined increase of Braarudosphaera bigelowii, the decrease of warm water coccolithophorid species and the increase of Reticulofenestra spp. This boundary is marked also by the reoccurrence of the planktonic foraminiferal species G. inflata and Neogloboquadrina pachyderma dextral and by an evident decrease of G. ruber var. rosea, indicating the end of the Holocene Climatic Optimum and the beginning of a cold and wet phase, probably corresponding to the Atlantic–Subboreal continental transition.

Palaeo-environmental variations in eastern Mediterranean sediments: a multidisciplinary approach in a prehistoric setting

Abstract Not only the occurrence of distinct organic-rich intervals (sapropels), but also the relative contents of key major and minor elements and isotopes in the sediments of the eastern Mediterranean, appear to be cyclic and to be astronomically associated. Interpretations of the environmental conditions leading to sapropel formation are based on results from sedimentological, micropalaeontological and geochemical studies of the dark-coloured layers and the cream/brownish sediments that occur above and below them. Part of the signal may be removed by early diagenetic processes. The extent and direction of these processes are ultimately controled by the amount and reactivity of organic matter. The interval of dark colour associated with a sapropel is often somewhat thicker than that defined by the >2% C org definition and usually has a sharp colour change at upper and lower boundaries. A grey so-called ‘proto-sapropel’ layer of variable thickness underlies most sapropel layers. A few centimeters above the most recent sapropel S1, is usually found a clear dark-brown layer 2–3 cm thickness is usually found, which has a diffuse, often mottled, upper boundary and a relatively abrupt colour transition at its lower boundary. The colour is characteristic of Mn oxyhydroxide enrichments. In the interval from the dark-brown layer to the visible upper S1 boundary, there is usually an increasingly red-brownish colour. The distinct upper manganese Marker-Bed has been related to the Santorini (Minoan) eruption in 3356±18 BP ( Bruins, H. J., & Van Der Plicht, J. (1996). The Exodus enigma. Nature, London , 382 , 213–214 ), but is more likely to be associated with a Basin-wide re-ventilation event induced by changing climatic (humidity) conditions. Using barite-Ba as a paleo-productivity indicator, enhanced fluxes, and hence increases in accumulation rates of organic carbon to the seafloor, must have occurred from approximately 9 to 5 ky BP. The perfect correlations between observed C org and calculated C org from the C org /Ba relation in the visible S1 interval, and the total lack of such correlation in the interval between the darkbrown layer and the visible S1 layer are remarkable. It seems, therefore, that S1 deposition lasted from 9 to 5 ky BP but the organic carbon for the upper part has been removed. The double barium peak visible in a number of sediments studied in high-resolution, may be related to the ‘Flooding’ of the Black Sea that occurred around 7150 BP (Ryan, W. B. F., Pittman, W. C., Major, C. O., Shimkus, K., Moskalenko, V., Jones, G. A., Dimitrov, P., Gorur, N., Sakinc, M., & Yuce, H. (1997). An abrupt drowning of the Black Sea shelf. Marine Geology, 138 , 119–126). Using various ‘proxies’, the (initial) occurrence of eastern Mediterranean sapropels appears cyclic and to be strongly related to the Monsoonal/Insolation Index. However, the relative value of an insolation maximum and initial C org content of the corresponding sapropel are not always related in a simple way. This again points to additional (possibly hydrographic) factors determining (the intensity of) sapropel formation. Understanding the mechanisms of sapropel formation and their subsequent preservation is not only necessary if our reconstructions of palaeoenvironmental conditions in the Eastern Mediterranean are to be improved, but may also assist in understanding the present-day situation and in forecasting possible future developments. The observed paleoenvironmental variations are discussed in a geochemical and environmental context, and are illustrated using typical examples from the eastern Mediteranean.

Mediterranean Ridge Accretionary Complex yields rich surprises

Exploration of the Mediterranean ridges extreme environments has led to several surprising findings. Over the last 10 years five brine lakes have been discovered in the deep Eastern Mediterranean. For the first time in the seas deep waters, a temperature of over 45°C was recorded in 1994 and evidence of a molluscan community possibly sustained by chemosynthesis was found in 1993.

Messinian paleogeography and erosional surfaces in Italy: an overview

Abstract The Messinian deposits of Italy display an extreme variability both lateral and vertical, including strong changes in salinity and in sediment accumulation rates. This variability strongly contrasts with the much more uniform nature of both the older (i.e. Tortonian) and younger (i.e. Zanclean) strata. Changes in salinity range from fresh water to hypersaline conditions, leading to evaporite precipitation (“salinity crisis”). The chloride facies it recorded in Calabria, facing the deep Ionian sea, in the central Sicilian Basin and in a single satellite basin of southern Tuscany, fed by the Ligurian Sea. Erosional surfaces are widespread at the southern edge of the Alps, and extend to the subsurface of the Po Basin. Rapidly subsiding, and outward moving foredeeps, deep-seated brine pools uplifted in post-Messinian times, post-tectonic extensional basins provide a different stratigraphic record of the same paleogeographic event, a dramatic drop of sea-level which lasted overall less than one million years.