No abstract

BackgroundNovosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome.ResultsPP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y’s phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly specialized metabolic pathways involved in: (i) aromatic hydrocarbon degradation; (ii) resistance to toxic compounds; and (iii) the quorum sensing mechanism.ConclusionsIn summary, the unraveling of the entire PP1Y genome sequence has provided important insight into PP1Y metabolism and, most importantly, has opened new perspectives about the possibility of its manipulation for bioremediation purposes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-384) contains supplementary material, which is available to authorized users.

Liver samples of 12 species of birds of different trophic levels, collected during the period 1998-2000 from coastal areas of the Campania region, Southern Italy, were analyzed for organochlorine pesticides (OCs), such as dichlorodiphenyltrichloroethane (DDT) and its metabolites, hexachlorobenzene (HCB), gamma-hexachlorocycloexane (gamma-HCH), aldrin, dieldrin, endrin, and the seven PCB "target" congeners, IUPAC Nos. 28, 52, 101, 118, 138, 153 and 180. p,p'-DDE was present in all the samples analyzed, at concentrations ranging from 4 to 4504 ng/g wet wt, which were much higher than those found for HCB, dieldrin, and p,p'-DDD. The concentrations of the others OCs were below the detection limit in all the samples. PCBs were found in all the bird species at levels ranging between 6 and 8431 ng/g wet wt. The hepta-, hexa-, and penta-chlorinated congeners 180, 153, 138, and 118 were predominant since, in almost all the species, they contributed to more than 98% of the total seven determined PCBs. No significant differences in mean concentrations of organochlorine pesticides are detected between single species or between species grouped according to their feeding habits (p > 0.05). However, p,p'-DDE levels were higher in carnivorous species than in omnivorous and insectivorous ones (carnivorous > omnivorous > insectivorous). Concentrations of total PCBs were significantly higher in omnivorous birds than in carnivorous (p < 0.01) and insectivorous ones (p < 0.001), whereas carnivorous birds exhibited significantly higher total PCB levels than insectivorous ones (p < 0.01). Marked differences in total PCB concentrations were found also between single species (from p < 0.05 to p < 0.001). Levels of OCs and PCBs were generally below the thresholds known to affect reproduction, however, mean hepatic concentrations of total PCBs in the yellow-legged herring gull (Larus cachinnans), black-headed gull (Larus ridibundus), and kestrel (Falcus tinnunculus) were far higher than those estimated to elicit immunosuppressive effects and possibly increase susceptibility to parasitoses.

In contrast to the widely accepted consensus of the existence of a single RNA polymerase in bacteria, several actinomycetes have been recently shown to possess two forms of RNA polymerases due the to co-existence of two rpoB paralogs in their genome. However, the biological significance of the rpoB duplication is obscure. In this study we have determined the genome sequence of the lipoglycopeptide antibiotic A40926 producer Nonomuraea gerenzanensis ATCC 39727, an actinomycete with a large genome and two rpoB genes, i.e. rpoB(S) (the wild-type gene) and rpoB(R) (the mutant-type gene). We next analyzed the transcriptional and metabolite profiles in the wild-type gene and in two derivative strains over-expressing either rpoB(R) or a mutated form of this gene to explore the physiological role and biotechnological potential of the “mutant-type” RNA polymerase. We show that rpoB(R) controls antibiotic production and a wide range of metabolic adaptive behaviors in response to environmental pH. This may give interesting perspectives also with regard to biotechnological applications.