a Whole Genome Array Approach - Jacobs University

Background
environmental genomics-project (REGX). REGX aims at understanding the adaptations of
marine bacteria to changing environmental conditions. Two sulphate reducing bacteria
(i.e.: Desulfotalea psychrophila and Desulfobacterium autotrophicum) and one Planctomycete
(Rhodopirellula baltica SH1 T ) were selected for whole genome sequencing, annotation and
functional analysis. The successful sequencing and annotation of the whole genome of the
Planctomycete R. baltica in 2003 (Glöckner et al. 2003) has established the framework for
further functional genomic analysis.
1.2 Planctomycetes
Planctomycetes are a group of budding, peptidoglycan-less bacteria with increasing
significance for microbial evolution, ecology, cell biology and genomics (Fuerst 1995). The
phylum consists of a single family (Planctomycetaceae) with six accepted (Rhodopirellula,
Blastopirellula, Pirellula, Planctomyces, Isosphaera, Gemmata) (Schlesner et al. 2004) and
four candidate genera (Kuenenia, Brocadia, Scalindua, Anammoxoglobus). Latest studies
group Planctomycetes with the PVC super phylum. This monophyletic clade is formed
besides the Planctomycetes by the phyla Chlamydiae, Verrrucomicrobia, Lentisphaerae and
the candidate phyla ‘Poribacter’and OP3 (Wagner and Horn 2006).
Most cultured strains so far have been isolated from terrestrial, freshwater and marine habitats
(Schlesner 1994; Fuerst 1995; Wang et al. 2002). In addition, studies based on cultivationindependent
molecular methods, e.g. Fluorescence in situ Hybridisation (Amann and Ludwig
2000), repeatedly confirmed the occurrence of Planctomycetes in terrestrial and aquatic
habitats (DeLong and Franks 1993; Chatzinotas et al. 1998; Neef et al. 1998; Vergin et al.
1998; Crump et al. 1999) and revealed an even broader distribution of the Planctomycetes in
the environment, e.g. in hot springs (Giovannoni et al. 1987), marine sponges (Fuerst et al.
1998; Fuerst et al. 1999; Pimentel-Elardo et al. 2003) as well as in hepatopancreas of the
crustacean Panaeus monodon (Fuerst et al. 1991; Fuerst et al. 1997). This shows the
successful colonisation of a broad spectrum of ecological niches by members of this phylum.
Further surveys reported the presence of Planctomycetes in marine-snow particles (Rath
1998) as well as in shallow and deep sea sediments of marine systems (Llobet-Brossa et al.
1998; Inagaki et al. 2006; Kirkpatrick et al. 2006; Musat et al. 2006). Morris and coworkers
showed that Planctomycetes appear and disappear with the blooming of diatoms (Morris et al.
2006). They postulate a direct interaction and carbon flow between the algae and
Planctomycetes. In addition, growth studies with R. baltica and other group members revealed
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