It is a microbial world we live in: microbes outnumber other organisms by several orders of magnitude, and they have great importance for the environment. However, environmental microbes are notoriously difficult to grow in the laboratory, and using culture independent techniques is necessary to expand our view. In this thesis, I apply metagenomics and single-cell genomics to environmental samples from ancient human remains and lakes. First, I used metagenomics to learn about bacteria from a Neanderthal’s bone and the gut of Ötzi, a frozen natural mummy. Both were exploratory studies where the main question was what kind of bacteria are present. I found out that Streptomyces dominated this particular Neanderthal fossil, and the DNA lacked the damage that is often seen in ancient samples. Ötzi's gut sample was dominated by Clostridia and fungi belonging to Basidiomycota. Second, ten single-cell amplified genomes of freshwater Alphaproteobacterium LD12 and three metagenomes from Swedish lakes were sequenced. Comparative metagenomics allowed hypothesizing about which functions are important for microbe proliferation in freshwater, pointing to osmoregulation and transport proteins and, possibly, to different strategies of metabolizing sugars. I also focused on SAR11 sister-groups in oceans and lakes. Phylogenies and sequence evolutionary distance estimates indicated the existence of microclusters within LD12, showing variation in abundance between lakes. The most striking difference was the relative amount of recombination compared to mutation, the estimated r/m ratio. SAR11 marine and their freshwater cousins are found at the opposite extremes of the r/m range, lowest and highest, respectively. The genetic background or sequence diversity did not explain the observed dramatic difference, so it is possibly connected to environmental adaptation or population dynamics. In addition, I have spent a substantial amount of effort benchmarking available metagenomic methods, for example fragment recruitment of metagenomes to reference genomes. In conclusion, my exploratory metagenomic studies have shed some light on the bacteria present in ancient human remains; comparative metagenomics has suggested the importance of substrate preference on functional differences between lakes and oceans; finally, single-cell genomes have allowed some insight into molecular evolutionary processes taking place in the freshwater LD12 bacterium.

Bacteria are mediators of biogeochemical cycles and are in this way vital for maintaining life on earth. Their distribution, abundance and functioning are driven by environmental heterogeneity and dynamic change in abiotic and biotic factors. Both, freshwater lakes and oceans play central roles in the global carbon cycle and bacteria in these systems perform many services for the ecosystems, such as the transfer of organic carbon from primary producers to higher trophic levels. With estimated relative abundances up to 50% of the total bacterioplankton, the Alphaproteobacteria lineage SAR11 is the most abundant group of aquatic bacteria. It is globally distributed and can be partitioned into multiple sub-clades, one of which is exclusive to freshwaters. Until recently, the distribution, abundance and ecological role of this freshwater SAR11 named LD12 was unknown. The aim of the thesis was to study the drivers and mechanisms that influence the dynamics of aquatic bacterial communities in general and the SAR11 and LD12 groups in particular. The thesis consists of environmental surveys of a mesotrophic Lake Erken and the western Southern Ocean, an experiment and a data-mining exercise to reveal the phylogenetic structure of the SAR11 lineage on various temporal and spatial scales. The analysis of a long-term bacterioplankton community survey in lake Erken provided insights about the dynamics of the entire bacterial community and the LD12 population over an annual cycle. The results demonstrate that LD12 can be an equally abundant member of freshwater communities as marine SAR11 in oceans. LD12 featured strong seasonality and was positively coupled to environmental conditions indicative for an oligotrophic lifestyle. LD12 as well as other dominant lake bacterioplankton also maintained stable populations throughout spatial and temporal varying environments, but at high phylogenetic resolution, habitat preferences were revealed, particularly in response to oxygen concentrations. The later was not the case in LD12 as a single ribotype dominated. This is in stark contrast to the habitat partitioning with light availability, depth and water masses observed for marine SAR11 subclades in the Southern Ocean. The global data-mining corroborated that LD12 as a group was much less diverse than SAR11 furthermore, suggesting that the marine-freshwater barrier acted as a population bottleneck. My work shows that bacterial populations can respond in very different ways to environmental drivers, highlight the importance of highly resolved temporal and spatial scales as well as the need for high phylogenetic resolutions to target ecologically coherent populations.