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

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. This infrastructure includes powerful hardware systems consisting of a computing cluster and dedicated servers. The appropriate software for data storage, access and analysis has been completely integrated. Open source solutions were selected for these tasks, which allows an optimal control of the system at very low exploitation costs. Additionally, the adoption of the corresponding open standards facilitate data exchange with other research institutes and constitute a solid basis for national and international collaborations. These computer infrastructures were built to annotate and analyze the genome of Pirellula sp. strain 1, but will also be used for the analysis of upcoming complete genomes of environmentally relevant microorganisms at the MPI-Bremen. Currently, local metagenomics projects already take advantage of the established annotation pipeline, as the bioinformatic methods needed for genomics and metagenomics are very similar. The genome of Pirellula sp. strain 1 was analyzed with bioinformatic methods and 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. This constitutes a proof of principle of the important role that whole genome analysis will play in the field of ecology in the future: the role of an “hypothesis generator”. Gene expression level predictions were calculated for Pirellula sp. strain 1, linking in silico analysis and functional genomics experiments. Transcriptome and proteome expression data will be compared to these predicted expression levels, which represents an untouched field for environmental organisms as such comparisons were only made for classical model organisms. 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 “genome trees” can be considered as a new, exploratory phylogenetic method and the differences between alternative phylogenetic reconstruction methods (e.g. 16S rRNA vs. full genomes) illustrates again the complexity of phylogenetic studies on Planctomycetes. 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.