Analysis of the Pseudoalteromonas tunicata genome reveals properties of a surface-associated life style in the marine environment.

BACKGROUND: Colonisation of sessile eukaryotic host surfaces (e.g. invertebrates and seaweeds) by bacteria is common in the marine environment and is expected to create significant inter-species competition and other interactions. The bacterium Pseudoalteromonas tunicata is a successful competitor on marine surfaces owing primarily to its ability to produce a number of inhibitory molecules. As such P. tunicata has become a model organism for the studies into processes of surface colonisation and eukaryotic host-bacteria interactions. METHODOLOGY/PRINCIPAL FINDINGS: To gain a broader understanding into the adaptation to a surface-associated life-style, we have sequenced and analysed the genome of P. tunicata and compared it to the genomes of closely related strains. We found that the P. tunicata genome contains several genes and gene clusters that are involved in the production of inhibitory compounds against surface competitors and secondary colonisers. Features of P. tunicata's oxidative stress response, iron scavenging and nutrient acquisition show that the organism is well adapted to high-density communities on surfaces. Variation of the P. tunicata genome is suggested by several landmarks of genetic rearrangements and mobile genetic elements (e.g. transposons, CRISPRs, phage). Surface attachment is likely to be mediated by curli, novel pili, a number of extracellular polymers and potentially other unexpected cell surface proteins. The P. tunicata genome also shows a utilisation pattern of extracellular polymers that would avoid a degradation of its recognised hosts, while potentially causing detrimental effects on other host types. In addition, the prevalence of recognised virulence genes suggests that P. tunicata has the potential for pathogenic interactions. CONCLUSIONS/SIGNIFICANCE: The genome analysis has revealed several physiological features that would provide P. tunciata with competitive advantage against other members of the surface-associated community. We have also identified properties that could mediate interactions with surfaces other than its currently recognised hosts. This together with the detection of known virulence genes leads to the hypothesis that P. tunicata maintains a carefully regulated balance between beneficial and detrimental interactions with a range of host surfaces.

Ecology of type II secretion in marine gammaproteobacteria.

Compelling findings on the direct association of the type II secretion (T2S) system with different ecological functions in marine bacteria have challenged the traditional view of the T2S pathway, the function of which has been mostly studied in pathogenic bacteria. The availability of a number of whole-genome sequence data sets enabled the analysis of the genetic composition of the T2S system across a number of Vibrios and Alteromonads. The widespread Gammaproteobacteria, in particular the Alteromonadales and the Vibrionales group, are recognized to play significant roles in the cycling of nutrients in coastal and pelagic marine ecosystems and are also found associated with marine eukaryotes. The combined analysis of the role and the genetic composition of the T2S system in Gammaproteobacteria provides important evidence for the significance of the T2S pathway in the ecology of environmental bacteria.

Profiling the secretome of the marine bacterium Pseudoalteromonas tunicata using amine-specific isobaric tagging (iTRAQ).

The eukaryote-associated marine bacterium Pseudoalteromonas tunicata produces a range of target-specific compounds that inhibit different types of marine organisms including invertebrate larvae and algal spores, as well as a broad spectrum of fungi, protozoa, and bacteria. The ability to produce such bioactive compounds is correlated to the expression of a yellow and a purple pigment in P. tunicata. To investigate the regulation and biosynthesis of the pigments and bioactive compounds, the expressed secretome of the pigmented wild-type P. tunicata and a nonpigmented mutant (wmpD-) defective in the type-II secretion pathway were compared. Secreted proteins were digested with trypsin, labeled using amine-specific isobaric tagging reagents (iTRAQ), and identified using two-dimensional SCX and nano C18 RP liquid-chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS). The iTRAQ labeling experiments enabled accurate measurement of the proteins identified in this work. A sequence-base prediction of P. tunicata secretome was also obtained and compared to the expressed proteome to determine the role of the type-II secretion pathway in this bacterium. Our results suggest that this secretion pathway has a role in iron transport and acquisition in P. tunicata.

Impact of oil contamination and biostimulation on the diversity of indigenous bacterial communities in soil microcosms.

The aim of this study was to analyse the effect of oil contamination and biostimulation (soil pH raise, and nitrogen, phosphate and sulphur addition) on the diversity of a bacterial community of an acidic Cambisol under Atlantic Forest. The experiment was based on the enumeration of bacterial populations and hydrocarbon degraders in microcosms through the use of conventional plating techniques and molecular fingerprinting of samples directly from the environment. PCR followed by denaturing gradient gel electrophoresis (DGGE) was used to generate microbial community fingerprints employing 16S rRNA gene as molecular marker. Biostimulation led to increases of soil pH (to 7.0) and of the levels of phosphorus and K, Ca, and Mg. Oil contamination caused an increase in soil organic carbon (170-190% higher than control soil). Total bacterial counts were stable throughout the experiment, while MPN counts of hydrocarbon degraders showed an increase in the biostimulated and oil-contaminated soil samples. Molecular fingerprinting performed with 16S rRNA gene PCR and DGGE analysis revealed stable patterns along the 360 days of experiment, showing little change in oil-contaminated microcosms after 90 days. The DGGE patterns of the biostimulated samples showed severe changes due to decreases in the number of bands as compared to the control samples as from 15 days after addition of nutrients to the soil. Results obtained in the present study indicate that the addition of inorganic compounds to soil in conjunction with oil contamination has a greater impact on the bacterial community than oil contamination only.