Suchergebnisse

Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes, and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared with freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities. ; This work was supported by the Swedish Foundation for Strategic Research (Grant Number ICA10-0015 to AE), the Swedish Research Council (Grant Numbers 349-2007-831, 621-2008-3259 and 621-2011-4669 to SGEA; 2009-3784, 2008-1923 and 2012-3892 to SB), the National Science Foundation [Awards CBET-0644949 (CAREER), MCB-0702653 (Microbial Observatories Program) to KD and DEB-841933 to RS], DEB-0822700 (Long Term Ecological Research, NTL LTER to KDM), the European Union (grant to SGEA), the Göran Gustafsson Foundation (grant to SGEA), the Knut and Alice Wallenberg Foundation (Grant Numbers KAW-2011.0148 and KAW-2012.0075 to SGEA), and the Swedish Wennergren Foundation (to KDM and SB).

Gene transfer agents (GTAs) randomly transfer short fragments of a bacterial genome. A novel putative GTA was recently discovered in the mouse-infecting bacterium Bartonella grahamii. Although GTAs are widespread in phylogenetically diverse bacteria, their role in evolution is largely unknown. Here, we present a comparative analysis of 16 Bartonella genomes ranging from 1.4 to 2.6 Mb in size, including six novel genomes from Bartonella isolated from a cow, two moose, two dogs, and a kangaroo. A phylogenetic tree inferred from 428 orthologous core genes indicates that the deadly human pathogen B. bacilliformis is related to the ruminant-adapted clade, rather than being the earliest diverging species in the genus as previously thought. A gene flux analysis identified 12 genes for a GTA and a phage-derived origin of replication as the most conserved innovations. These are located in a region of a few hundred kb that also contains 8 insertions of gene clusters for type III, IV, and V secretion systems, and genes for putatively secreted molecules such as cholera-like toxins. The phylogenies indicate a recent transfer of seven genes in the virB gene cluster for a type IV secretion system from a cat-adapted B. henselae to a dog-adapted B. vinsonii strain. We show that the B. henselae GTA is functional and can transfer genes in vitro. We suggest that the maintenance of the GTA is driven by selection to increase the likelihood of horizontal gene transfer and argue that this process is beneficial at the population level, by facilitating adaptive evolution of the host-adaptation systems and thereby expansion of the host range size. The process counters gene loss and forces all cells to contribute to the production of the GTA and the secreted molecules. The results advance our understanding of the role that GTAs play for the evolution of bacterial genomes. ; The authors have been supported by grants to SGEA from the European Union (QLK3-CT2000-01079, EUWOL and EuroPathogenomics), the Swedish Research Council (315-2004-6676), the Göran Gustafsson Foundation, and the Knut and Alice Wallenberg Foundation. LG is supported by grants from the Swiss National Science Foundation (PBLA33-119626 and PA00P3_131491) and the Swedish Research Council (623-2009-743). ; Peer reviewed