FREDI_Ecological diversification within the subspecies Polynucleobacter necessarius ssp. asymbioticus and environmental ecotype sorting

The major aim of Individual Project IP-02 is to reveal and understand microevolutionary mechanisms resulting in ecological diversification of phylogenetically narrow groups of planktonic freshwater bacteria enabling colonization of broad ranges of habitat types by phylogenetically narrow groups. Insights in these processes and mechanisms are essential for a comprehensive understanding of diversity and function of bacterial communities in natural ecosystems. Bacteria of the subspecies Polynucleobacter necessarius ssp. asymbioticus (Betaproteobacteria) were selected as a model group for the intended investigations. This subspecies represents planktonic bacteria dwelling in lentic freshwater habitats (ponds and lakes) and is also present in larger running water systems (streams). The subspecies has a cosmopolitan distribution, and comprises up to 67% of total cell numbers of bacterioplankton. The subspecies is ubiquitously present in all kinds of lentic freshwater systems, which includes, for instance, acidic bog systems, as well as alkaline lakes and ponds. On the first look, such a wide distribution and especially the ubiquitous occurrence seems to indicate a very high ecological tolerance and a superior competitiveness of the subspecies, however, the ecological success of the subspecies is rather a result of ecological radiation in ecotypes adapted to different ecological niches. It was demonstrated, for instance, that some ecotypes are adapted to the environmental conditions in acidic habitats, while others are adapted to conditions in alkaline hardwater lakes, which is resulting in complete niche separation between these ecotypes. Additionally, the existence of geotypes characterized by restricted geographic distributions was demonstrated. The microevolutionary mechanisms driving the radiation in ecotypes and geotypes shall be investigated by means of genome sequencing and analyses. The genomes of ten selected strains representing different eco- and geotypes will be genome sequenced (draft quality, 454 pyrosequencing). The selected strains were obtained from acidic bog systems, alkaline clear water lakes, high-mountain lakes, tropical habitats, and a lake located in Antarctica. Assembly of the draft genomes will be supported by the availability of the complete genome sequence of another strain belonging to the investigated subspecies. This genome sequence will be used as a template for the assembly of the ten genomes. Comparative genome analyses will reveal if the major driver of the microevolution of the subspecies is the acquisition of foreign adaptive genes by horizontal gene transfer, or the ecological optimization of the own genetic makeup by mutation and homologous recombination. Furthermore, the environmental distribution of eco- and geotypes will be investigated newly developed qPCR assays. The genomic data established in this Individual Project (IP-2) will be essential for the Individual Projects IP-1, IP-4, and IP-5. These projects will utilize the delivered genome data for revealing the ecological function (e.g., within the carbon cycle) of Polynucleobacter bacteria, as well as their adaptation to oxidative stress. Feasibility of IP-2 will crucially depend on the employment of a PostDoc with excellent bioinformatics skills. Such skills will be essential for genome assembly and comparative genome analyses.

The major goal of the project was the investigation of the ecological diversification within a group of bacteria, dwelling in the water column of freshwater systems (lakes and ponds). When the project started, it was assumed that the investigated group represents only a subgroup of the species Polynucleobacter necessarius. This was suggested by previous phylogenetic and taxonomic research. Surprisingly, comparative genome analyses conducted in the course of the project revealed that this subgroup actually represents a large cryptic species complex. Our investigations resulted in the discovery of 70 so far undescribed species. A large fraction of these new species is dwelling in freshwater systems located in Austria and neighboring countries. The analyses of the genomes of Polynucleobacter bacteria resulted in the identification of various genes involved in adaptation to diverse environmental conditions. One example are genes involved in adaptation to acidic or alkaline lakes or ponds. The results gained in this project enable detailed new insights in evolution and diversity of freshwater bacteria. Furthermore, these results will drive a large taxonomic revision of the genus Polynucleobacter.