Prokaryotes

Next-generation sequencing studies have revealed that a variety of transcripts are present in the prokaryotic transcriptome and a significant fraction of them are functional, being involved in various regulatory activities apart from coding for proteins. Identification of promoters associated with different transcripts is necessary for characterization of the transcriptome. Promoter regions have been shown to have unique structural features as compared with their flanking region , in organisms covering all domains of life. Here we report an in silico analysis of DNA sequence dependent structural properties like stability, bendability and curvature in the promoter region of six different prokaryotic transcriptomes. Using these structural features, we predicted promoters associated with different categories of transcripts (mRNA, internal, antisense and non-coding), which constitute the transcriptome. Promoter annotation using structural features is fairly accurate and reliable with about 50% of the primary promoters being characterized by all three structural properties while at least one property identifies 95%. We also studied the relative differences of these structural features in terms of gene expression and found that the features , viz. lower stability, lesser bendability and higher curvature are more prominent in the promoter regions which are associated with high gene expression as compared with low expression genes. Hence, promoters, which are associated with higher gene expression, get annotated well using DNA structural features as compared with those, which are linked to lower gene expression.

The Ionian Sea represents a suitable basin for studying the biogeochemical processes mediated by microbial
activities. Because of its characteristics as a crossing region between the western and eastern Mediterranean
Sea, it is one of the sites most affected by changes in water mass composition and dynamics, caused by the Eastern Mediterranean Transient (EMT). To date, relatively few data exist on microbial activities in pelagic areas of the Ionian Sea. From 1998 to 2004, during different research cruises, prokaryotic parameters
(abundance, extracellular enzyme activities leucine aminopeptidase, β-glucosidase, alkaline phosphatase,
bacterial production and respiration) were measured together with culturable bacteria and the main physical,
chemical and trophic parameters (temperature, salinity, nutrients, particulated organic matter). The aim of
the study was to describe the spatial and temporal variability in microbial activities involved in the carbon
and phosphorus cycles, in different layers. Results showed that organic matter transformation mediated
by the microbial community displayed a significant increase in autumn, highlighting the occurrence of significant changes at meso- and bathypelagic depths. Unlike the dark ocean, bacterial growth efficiency in the Ionian Sea, which increased with depth, seemed to vary from being a source of carbon in the epipelagic
layer to a sink in the meso- and bathypelagic layers. The mechanism of phosphatase regulation showed a
weak inverse correlation between specific phosphatase and inorganic P in all seasons except autumn. It is worth mentioning that the reported results constitute, to the best of our knowledge, one of the available datasets giving information about microbial activities in the Ionian Sea.

The southern- central Tyrrhenian Sea is a poorly studied area of the Mediterranean Sea, although its importance
for the biological fluxes among the western and eastern basins is recognised. This note aimed at evaluating in the
waters of the Southern Tyrrhenian Sea the efficiency of some steps of the organic matter processing (enzymatic
hydrolysis, prokaryotic production and oxidation) and the role played by the prokaryotic community in this context.
During the MEDBIO multidisciplinary cruise performed in July 2005, the distribution of prokaryotic abundance and
activities (exoenzymatic activity, heterotrophic production and respiratory activity) was studied. The results showed
the presence of high exoenzymatic activity rates (mostly leucine aminopeptidase) in the deep sea, while heterotrophic
production and respiratory activity rates were high at surface. Some speculations on the different behaviors of the
Carbon fluxes occurring among the different epi-, meso- and bathypelagic layers are reported. At the epipelagic layer
both the decomposition and biomass production processes were high. At the mesopelagic layer the organic matter was
quickly mobilised but not efficiently incorporated into biomass, therefore the dissolved monomers remained available
in the water column for export to other trophic levels or utilization in other chemical processes (lateral advection,
oxidation). The bathypelagic layer was characterised by high levels of hydrolytic activity coupled with relatively high
prokaryotic production; in this layer, exoenzymatic activity levels fall in an order of magnitude similar to that observed
at the epipelagic one. This finding highlights the importance of microbially mediated processes in sustaining life in the
marine depths.