The genome of the free-living, marine Planctomycete Pirellula sp. strain 1 ( Rhodopirellula baltica ): Bioinformatics and Biology

Abstract

The complete genome analysis of environmentally relevant microorganisms constitute a new emerging field of marine research. Within the frame of this work, the bioinformatic infrastructures adapted to microbial genomics data have been locally established at the Department of Molecular Ecology of the MPI-Bremen and the complete genome of a bacteria - Pirellula sp. strain 1 - was annotated.Pirellula sp. strain 1 is a marine bacteria belonging to the phylum Planctomycetes and the bioinformatics analysis of its genome revealed the blueprint of this organism containing unexpected findings. The occurrence of an outstanding number of sulfatases gene copies and of an unexpected Archaea-like C1 metabolism are some examples of annotation highlights. Based on these new data, hypothesis concerning the lifestyle and the evolution of this organism, and more broadly of Planctomycetes, could be formulated. Gene expression level predictions were calculated for Pirellula sp. strain 1, linking in silico analysis and functional genomics experiments.The availability of the first complete genome of a Planctomycete allowed to reassess the phylogenetic position of this phylum by using genome trees . This new approach did not support the previously suggested deepest branching position of the Planctomycetes within the bacterial domain by particular 16S rDNA analysis and retained the thermophilic organisms as deepest branching.The importance of the emerging field of environmental metagenomic studies as an indispensable companion of the whole genome sequencing of isolated strain becomes evident today. Just as the number of complete genomes, the number of available metagenomics sequences is expected to explode within the next years. A geographic information system (GIS) for metagenomics data was developed and represents a first prototype of specialized database and tools to handle this new kind of data.