Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations

We report the genetic organisation of six prophages present in the genome of Lactococcus lactis IL1403. The three larger prophages (36–42 kb), belong to the already described P335 group of temperate phages, whereas the three smaller ones (13–15 kb) are most probably satellites relying on helper phage(s) for multiplication. These data give a new insight into the genetic structure of lactococcal phage populations. P335 temperate phages have variable genomes, sharing homology over only 10–33% of their length. In contrast, virulent phages have highly similar genomes sharing homology over >90% of their length. Further analysis of genetic structure in all known groups of phages active on other bacterial hosts such as Escherichia coli, Bacillus subtilis, Mycobacterium and Streptococcus thermophilus confirmed the existence of two types of genetic structure related to the phage way of life. This might reflect different intensities of horizontal DNA exchange: low among purely virulent phages and high among temperate phages and their lytic homologues. We suggest that the constraints on genetic exchange among purely virulent phages reflect their optimal genetic organisation, adapted to a more specialised and extreme form of parasitism than temperate/lytic phages.

Phosphorus dynamics in waters of the Pacific Ocean

Tagged phosphorus was used to measure principal indices of mineral phosphorus variations in the euphotic zone of the East Pacific, i.e. total rate of uptake of phosphate phosphorus by microplankton (A_t), fraction consumed by phytoplankton (A_p/A_t), and turnover time (T). A_t reached its greatest values (150-280 ng/l/hour) in the upwelling zone of the Peru traverse, where development of phytoplankton was induced by upwelling. In other areas of this traverse values were 40-80 ng/l/hour in surface layers. In less productive waters on two other profiles (off Central America and California), values were lower, between 20 and 40 ng/l. On the vertical profile maxima of A_t were found at the upper boundary of the thermocline. Turnover time of PO4 phosphorus (T) in zones of phytoplankton abundance was very short, between 1.5 and 4 days. At most other stations it was 10-40 days, increasing to 100-200 days or longer at the lower boundary of the euphotic zone. In areas of phytoplankton abundance it accounted for 60-80% of total uptake of PO4 phosphorus. But in zones of elevated bacterial abundance, A_p/A_t fell to 20-40%. Data indicating lack of correlation between PO4 phosphorus and productivity are presented. It is emphasized that the above measures of PO4 phosphorus dynamics can be used for obtaining measures of functional condition and successional phase of marine plankton communities.

Dissipative Raman solitons

A new type of dissipative solitons - dissipative Raman solitons - are revealed on the basis of numerical study of the generalized complex nonlinear Ginzburg-Landau equation. The stimulated Raman scattering significantly affects the energy scalability of the dissipative solitons, causing splitting to multiple pulses. We show, that an appropriate increase of the group-delay dispersion can suppress the multipulsing instability due to formation of the dissipative Raman soliton, which is chirped, has a Stokes-shifted spectrum, and chaotic modulation on its trailing edge. The strong perturbation of a soliton envelope caused by the stimulated Raman scattering confines the energy scalability, preventing the so-called dissipative soliton resonance. We show that in practical implementations, a spectral filter can extend the stability regions of high-energy pulses.

Pore-water concentration of chloride in sediment cores and equilibrium temperatures and gas bubble analysis at ROV stations from the Vodyanitskii mud volcano

Vodyanitskii mud volcano is located at a depth of about 2070 m in the Sorokin Trough, Black sea. It is a 500-m wide and 20-m high cone surrounded by a depression, which is typical of many mud volcanoes in the Black Sea. 75 kHz sidescan sonar show different generations of mud flows that include mud breccia, authigenic carbonates, and gas hydrates that were sampled by gravity coring. The fluids that flow through or erupt with the mud are enriched in chloride (up to 650 mmol L**-1 at 150-cm sediment depth) suggesting a deep source, which is similar to the fluids of the close-by Dvurechenskii mud volcano. Direct observation with the remotely operated vehicle Quest revealed gas bubbles emanating at two distinct sites at the crest of the mud volcano, which confirms earlier observations of bubble-induced hydroacoustic anomalies in echosounder records. The sediments at the main bubble emission site show a thermal anomaly with temperatures at 60 cm sediment depth that were 0.9 °C warmer than the bottom water. Chemical and isotopic analyses of the emanated gas revealed that it consisted primarily of methane (99.8%) and was of microbial origin (dD-CH4 = -170.8 per mil (SMOW), d13C-CH4 = -61.0 per mil (V-PDB), d13C-C2H6 = -44.0 per mil (V-PDB)). The gas flux was estimated using the video observations of the ROV. Assuming that the flux is constant with time, about 0.9 ± 0.5 x 10**6 mol of methane is released every year. This value is of the same order-of-magnitude as reported fluxes of dissolved methane released with pore water at other mud volcanoes. This suggests that bubble emanation is a significant pathway transporting methane from the sediments into the water column.

(Table 1) Chemical and isotopic composition of pore fluids in cores TGC-1 and TGC-6

The role of sediment diagenesis in the marine cycles of Li and B is poorly understood. Because Li and B are easily mobilized during burial and are consumed in authigenic clay mineral formation, their abundance in marine pore waters varies considerably. Exchange with the overlying ocean through diffusive fluxes should thus be common. Nevertheless, only a minor Li sink associated with the low-temperature alteration of volcanic ash has been observed. We describe a low-temperature diagenetic environment in the Black Sea dominated by the alteration of detrital plagioclase feldspars. Fluids expelled from the Odessa mud volcano in the Sorokin Trough originate from shallow (~100-400 m deep) sediments which are poor in volcanic materials but rich in anorthite. These fluids are depleted in Na+, K+, Li+, B, and 18O and enriched in Ca2+ and Sr2+, indicating that anorthite is dissolving and authigenic clays are forming. Using a simple chemical model, we calculate the pH and the partial pressure of CO2 (PCO2) in fluids associated with this alteration process. Our results show that the pH of these fluids is up to 1.5 pH units lower than in most deep marine sediments and that PCO2 levels are up to several hundred times higher than in the atmosphere. These conditions are similar to those which favor the weathering of silicate minerals in subaerial soil environments. We propose that in Black Sea sediments enhanced organic matter preservation favors CO2 production through methanogenesis and results in a low pore water pH, compared to most deep sea sediments. As a result, silicate mineral weathering, which is a sluggish process in most marine diagenetic environments, proceeds rapidly in Black Sea sediments. There is a potential for organic matter-rich continental shelf environments to host this type of diagenesis. Should such environments be widespread, this new Li and B sink could help balance the marine Li and Li isotope budgets but would imply an apparent imbalance in the B cycle.

Temperature measurements, gas chemistry, and gas hydrates of the Dvurechenskii mud volcano

The sediment temperature distribution at mud volcanoes provides insights into their activity and into the occurrence of gas hydrates. If ambient pressure and temperature conditions are close to the limits of the gas hydrate stability field, the sediment temperature distribution not only limits the occurrence of gas hydrates, but is itself influenced by heat production and consumption related to the formation and dissociation of gas hydrates. Located in the Sorokin Trough in the northern Black Sea, the Dvurechenskii mud volcano (DMV) was in the focus of detailed investigations during the M72/2 and M73/3a cruises of the German R/V Meteor and the ROV Quest 4000 m in February and March 2007. A large number of in-situ sediment temperature measurements were conducted from the ROV and with a sensor-equipped gravity corer. Gas hydrates were sampled in pressurized cores using a dynamic autoclave piston corer (DAPC). The thermal structure of the DMV suggests a regime of fluid flow at rates decreasing from the summit towards the edges of the mud volcano, accompanied by intermittent mud expulsion at the summit. Modeled gas hydrate dissociation temperatures reveal that the gas hydrates at the DMV are very close to the stability limits. Changes in heat flow due to variable seepage rates probably do not result in changes in sediment temperature but are compensated by gas hydrate dissociation and formation.