Proteorhodopsin Phototrophy Promotes Survival of Marine Bacteria during Starvation

Mutational analysis provides direct evidence for the link between proteorhodopsin light-harvesting and enhanced survival of marine bacteria

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria 'that rule the waves' (LD12)

Alphaproteobacteria are common members of marine bacterioplankton assemblages, but are believed to be rare in lacustrine systems. However, uncultured Alphaproteobacteria of the freshwater LD12 lineage form a tight monophyletic sister group with the numerically dominant bacteria in marine epipelagic waters, the SAR11 clade or genus Pelagibacter. Comparative rRNA sequence analysis reveals a global occurrence of LD12 bacteria in freshwater systems. The association of genotypic subclades with single-study systems moreover suggests a regional diversification. LD12 bacteria exhibit distinct and annually recurring spatio-temporal distribution patterns in prealpine lakes, as assessed by seasonally resolved vertical profiling and high-throughput cell counting. During the summer months, these ultramicrobacteria can form cell densities in the surface (epilimnetic) water layers that are comparable to those of their marine counterparts (>5 x 10(8) cells per l). LD12 bacteria had a pronounced preference for glutamine and glutamate over 7 other amino acids in situ, and they exhibited substantially higher uptake of these two substrates (and glycine) than the microbial assemblage in general. In addition, members of LD12 were also able to exploit other monomeric sources of organic carbon such as glucose, fructose or acetate. LD12 seemed to follow an oligotrophic lifestyle with slow but efficient uptake already at low substrate concentrations. Thus, LD12 bacteria do not only share phenotypic and metabolic traits with Pelagibacter, but also seem to thrive in the analogous spatiotemporal niche in freshwaters. The two groups together form one of the rare monophyletic lineages of ultramicrobacteria that have successfully traversed the barrier between marine and freshwater habitats. The ISME Journal (2011) 5, 1242-1252; doi:10.1038/ismej.2011.8; published online 17 March 201

Widespread distribution of proteorhodopsins in freshwater and brackish ecosystems

Proteorhodopsins (PRs) are light-driven proton pumps that have been found in a variety of marine environments. The goal of this study was to search for PR presence in different freshwater and brackish environments and to explore the diversity of non-marine PR protein. Here, we show that PRs exist in distinctly different aquatic environments, ranging from clear water lakes to peat lakes and in the Baltic Sea. Some of the PRs observed in this study formed unique clades that were not previously observed in marine environments, whereas others were similar to PRs found in non-marine samples of the Global Ocean Sampling (GOS) expedition. Furthermore, the similarity of several PRs isolated from lakes in different parts of the world suggests that these genes are dispersed globally and that they may encode unique functional capabilities enabling successful competition in a wide range of freshwater environments. Phylogenomic analysis of genes found on these GOS scaffolds suggests that some of the freshwater PRs are found in freshwater Flavobacteria and freshwater SAR11-like bacteria