Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment

Abstract

BackgroundColonisation 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 FindingsTo 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/SignificanceThe 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.

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

“…The type of microbe-host interaction of P. gallaeciensis may be mutualistic as well as pathogenic, as suggested by Seyedsayamdost et al (2011). The latter is supported by several virulenceassociated features like the type IV secretion system or siderophore production and was also stated for other marine bacteria (Thomas et al, 2008). The apparently highly defined habitat specificity of the two strains has selected for a very similar genomic design despite the great geographic distance.…”

Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913

“…The deep-sea sedimentary bacterium S. piezotolerans WP3 contains a LF gene cluster that is upregulated at low temperatures (Wang et al, 2008), whereas the surface-sea bacteria Pseudoalteromonas tunicata D2 and Alteromonadales sp. TW-7 both lack the LF gene cluster (Thomas et al, 2008). Generally, it seems that deep-sea sedimentary bacteria usually have the LF gene cluster, whereas related surface bacteria lack it.…”

“…This operon is absent in TAC125 and conserved in Alteromonadales sp. TW-7 and P. tunicata D2 (Thomas et al, 2008). Bacterial glycogen is considered to be a storage product that provides both energy and carbon during starvation periods (Strange, 1968;Preiss, 1984).…”

“…For example, the complete genome sequence analysis of P. haloplanktis TAC125 reflects its ability to cope with cold in Antarctic sea water (Médigue et al, 2005). Genome analysis of Pseudoalteromonas tunicata isolated from the surface of marine alga reflects its surface-associated marine lifestyle (Thomas et al, 2008). Comparative genomics is a powerful tool for understanding the ecological specialization of different ecotypes, which may shed light on the specific adaptations that bacteria make in different microenvironments (Ting et al, 2002;Kettler et al, 2007;Ivars-Martinez et al, 2008).…”

Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1

“…Pseudoalteromonads are ubiquitous heterotrophic members of marine bacterial communities, which, as with most microbial life, are ecologically and evolutionarily influenced by phages (Moebus, 1992;Wichels et al, 1998Wichels et al, , 2002Männistö et al, 1999;Médigue et al, 2005;Thomas et al, 2008). All three sequenced Pseudoalteromonads contain integrated prophages, two of which are dominated by P2-like myovirus proteins (Prophinder) (Lima-Mendez et al, 2008).…”