Effects and Dynamics of Insertion Sequences in the Evolution of Cyanobacteria

Abstract: Cyanobacteria are globally widespread and ecologically highly significant photoautotrophic microorganisms, with diverse geno- and phenotypic characters unprecedented among prokaryotes. This phylum embraces representatives with an exclusive adaptability in highly specialized environments, from oligotrophic ocean waters to the interior of cells in symbiotic plants, the most extreme being the chloroplasts. Insertion sequences (ISs) are short (~1000 bp) mobile genetic elements prevalent in microbial genomes, potentially representing potent adaptive forces.In this thesis, hypotheses tested that ISs play significant roles in both reductive and adaptive evolution in physiologically versatile cyanobacteria, using two model systems. First, the genome of an obligate plant (Azolla) symbiont, the cyanobacterium ‘Nostoc azollae 0708’, was sequenced, which led to the discovery of a highly ‘eroding’ genome (5,48 Mbp), loaded with ISs covering 14% of the genome, a situation likely caused by the relaxed selection pressure within the plant. The ISs were located in close proximity to the extremely numerous pseudogenes identified, although genes with key functions in a symbiotic context escaped IS mediated erosion (e.g. nitrogen fixation and differentiation genes). Some ISs were shown to have transposed short distances within the genome (‘local hoping’), and to be likely causative agents in pseudogene formation, and thus pivotal actors in the reductive evolution discovered.To widen the scope of ISs further, additionally 66 phylogenetically diverse microorganisms with a variety of life styles (free-living, symbionts, pathogens) were examined in regards to ISs influence. The data verified their over-all importance in shaping microbial genomes.Finally, natural microbial populations in the Baltic Sea, a semi-enclosed geologically young (~10,000 years) brackish water body offering steep gradients in salinity and nutrient loads, were examined using metatranscriptomics and metagenomics. A large proportion of the metagenome was devoted to ISs and most importantly a large fraction of the metatranscriptome consisted of IS transcripts (~1%), which may be suggestive of a high IS activity. These phenomena were most apparent in cyanobacteria in central parts of the Baltic Sea. The presence of an especially rich abundance of ISs in brackish waters was further substantiated by their low frequency (< 0.1%) in microbes of marine waters. Hence, ISs may facilitate both adaptations (short term) and adaptive evolution (long term) in microbes entering brackish water, otherwise unable to cross the distinct limnic-to-marine salinity-divide. Together, the data reveal high genomic loads of ISs in cyanobacteria subject to highly demanding conditions and stress the importance of locally migrating ISs (and pseudogenization) as important facilitators in adaptation and evolution, being a more rapid process than hitherto expected. The findings strongly support current theories stating a crucial role of ISs in shaping microbial genomes to render fitness.