Genomics of bacterial adaptations

The ecological and genetic factors governing bacterial adaptations to environmental conditions are not well known. One reason for this lack of knowledge is that only a small fraction of bacteria can be cultivated. New approaches based on single cell and metagenomic methods have started to give a glimpse of the microbial diversity present on Earth.

We have used these new methods to extend our previous studies of obligate host-adapted bacteria. We have identified new molecular systems that shuffle DNA between bacterial populations, such as the gene transfer agent in Bartonella. We have also studied bacterial speciation processes in bacteria adapted to the same versus different host species, with a specific focus on Wolbachia adapted to a variety of different Drosphila species.

As part of the UCEG environment, new collaborative research projects have been initiated between Andersson and associate members of UCEG. One such new collaborative research project is on the SAR11 group of bacteria that dominate the upper surface waters of the world´s oceans. These bacteria are key players in the ocean carbon cycle and represent about 25% of cells in coastal, estuary and open-ocean habitats. Genome sizes are less than 1.5 Mb, thus approaching the sizes of obligate host-adapted bacteria. Despite its abundance and global importance, the SAR11 group of bacteria is taxonomically not well defined. We have recently shown that the SAR11 clade clusters with other free-living bacteria in soil and aquatic systems rather than with obligate intracellular bacteria, as previously suggested.

SAR11 contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet.We isolated and sequenced single SAR11 cells from freshwater lakes. We have shown that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. Metagenome sequence data from both Swedish and American lakes have confirmed low recombination frequencies and revealed lake-specific variations in microcluster abundances. This is remarkable since members of the marine SAR11 clade have one of the highest ratios. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.

Recent publications

Zaremba-Niedzwiedzka, K., Viklund, J., Zhao, W., Ast, J., Sczyrba, A., Woyke, T., McMahon, K., Bertilsson, S., Stepanauskas, R. and S. G. E. Andersson. 2013. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biol. In press.

Eiler, A., Zaremba-Niedzwiedzka, K., Garcia, M. M., McMahon, K. D., Stepanauskas, R., Andersson, S. G. E., Bertilsson, S. 2013. Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics. Environ. Microbiol. Epub ahead of print.

Viklund, J., Martijn, J., Ettema, J. G. and S. G. E. Andersson. 2013. Comparative and phylogenomic evidence that the alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade. PLoS One 8:e78858.

Viklund, J., Ettema, T. J. and S. G. E. Andersson. 2012. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 29:599-615.

Brindefalk, B., Ettema, T. J., Viklund, J., Thollesson, M. and S. G. E. Andersson.2011. A phylometagenomic exploration of oceanic alpha-proteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade. PLoS One. 6:e24457.

Ellegaard, K. M., Klasson, L. and S. G. E. Andersson. 2013. Testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations. PLoS One In press.

Guy, L., Nystedt, B., Toft, C., Zaremba, K., Berglund, E., Granberg, F., Näslund, K., Eriksson, A.-S. and S. G. E. Andersson. 2013. A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella. PLoS Genet. 9:e1003393.

Ellegaard, K., Klasson, L., Näslund, K., Bourtzis, K. and S. G. E. Andersson. 2013. Comparative genomics of Wolbachia and the bacterial species concept. PLoS Genet. 9:e10033881.

Guy, L., Jernberg, C., Ivarsson, S., Hedenström, I., Engstrand, L. and S. G. E. Andersson. 2012. Genomic diversity of the 2011 European outbreaks of Escherichia coli O104:H4. Proc. Natl. Acad. Sci. USA 109:E3627-3628.