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Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.

Culturability and coexistence of bacterioplankton exhibiting different life strategies were investigated in the Baltic Sea and Skagerrak Sea. Bacterial numbers were estimated using a dilution-to-extinction culturing assay (DCA) and calculated as the most probable number, based on six different methods to detect bacterial growth in the DCA. Irrespective of the method used to detect growth, the fraction of multiplying cells never exceeded 10%, using the total count of 4′,6′-diamidino-2-phenylindole (DAPI)-stainable cells as a reference. Furthermore, the data also showed that non-colony-forming bacteria made up the majority of the viable cells, confirming molecular results showing dominance of non-colony-forming bacteria in clone libraries. The results obtained are in agreement with previous observations, indicating that bacterial assemblages in seawater are dominated by small, active subpopulations coexisting with a large group of inactive cells. The ratio of colony-forming to non-colony-forming bacteria was approximately 10 to 20 times higher in the brackish Baltic Sea than in the Skagerrak Sea. These two sea areas differ in (for example) their levels of bacterial production, dissolved organic carbon, and salinity. We suggest that the relative importance of colony-forming versus non-colony-forming bacterioplankton may be linked to environmental characteristics.

The coupling between the presence of predominant bacterial species and particular biogeochemical processes is of primary interest in current microbial ecology. Molecular methods such as microarrays and real-time polymerase chain reaction (PCR) may be used to estimate presence or expression of different genes (e.g., 16S rDNA and nifH) in environmental samples; however, to be quantitative, these methods require a reproducible and efficient DNA extraction protocol. Using picogreen DNA quantification, real-time PCR, and an internal DNA standard, we step-wise examined and optimized a protocol for DNA extraction from centrifuged or filtered seawater samples (vol. 2 to 300 mL). Sample volume had a pronounced effect on DNA extraction efficiency showing that comparison of samples with different volumes is problematic. The duration of enzyme treatment (lysozyme and proteinase K) significantly influenced the DNA extraction efficiency. Dissolved DNA contributed significantly to total DNA when extracted from small filtering volumes (

Viral lysis of specific bacterial populations has been suggested to be an important factor for structuring marine bacterioplankton communities. In the present study, the influence of bacteriophages on the diversity and population dynamics of four marine bacterial phage-host systems was studied experimentally in continuous cultures and theoretically by a mathematical model. By use of whole genome DNA hybridization toward community DNA, we analyzed the dynamics of individual bacterial host populations in response to the addition of their specific phage in continuous cultures of mixed bacterial assemblages. In these experiments, viral lysis had only temporary effects on the dynamics and diversity of the individual bacterial host species. Following the initial lysis of sensitive host cells, growth of phage-resistant clones of the added bacteria resulted in a distribution of bacterial strains in the phage-enriched culture that was similar to that in the control culture without phages after about 50-60 h incubation. Consequently, after a time frame of 5-10 generations after lysis, it was the interspecies competition rather than viral lysis of specific bacterial strains that was the driving force in the regulation of bacterial species composition in these experiments. The clonal diversity, on the other hand, was strongly influenced by viral activity, since the clonal composition of the four species in the phage-enriched culture changed completely from phage-sensitive to phage-resistant clones. The model simulation predicted that viral lysis had a strong impact on the population dynamics, the species composition, and the clonal composition of the bacterial community over longer time scales (weeks). However, according to the model, the overall density of bacteria in the system was not affected by phages, since resistant clones complemented the fluctuations caused by viral lysis. Based on the model analysis, we therefore suggest that viral lysis can have a strong influence on the dynamics of bacterial populations in planktonic marine systems.

The Baltic Sea is one of the largest brackish environments on Earth. Despite extensive knowledge about food web interactions and pelagic ecosystem functioning, information about the bacterial community composition in the Baltic Sea is scarce. We hypothesized that due to the eutrophic low-salinity environment and the long water residence time (>5 years), the bacterioplankton community from the Baltic proper shows a native “brackish” composition influenced by both freshwater and marine phylotypes. The bacterial community composition in surface water (3-m depth) was examined at a single station throughout a full year. Denaturing gradient gel electrophoresis (DGGE) showed that the community composition changed over the year. Further, it indicated that at the four extensive samplings (16S rRNA gene clone libraries and bacterial isolates from low- and high-nutrient agar plates and seawater cultures), different bacterial assemblages associated with different environmental conditions were present. Overall, the sequencing of 26 DGGE bands, 160 clones, 209 plate isolates, and 9 dilution culture isolates showed that the bacterial assemblage in surface waters of the central Baltic Sea was dominated by Bacteroidetes but exhibited a pronounced influence of typical freshwater phylogenetic groups within Actinobacteria , Verrucomicrobia , and Betaproteobacteria and a lack of typical marine taxa. This first comprehensive analysis of bacterial community composition in the central Baltic Sea points to the existence of an autochthonous estuarine community uniquely adapted to the environmental conditions prevailing in this brackish environment.

Formation of a biofilm or colony by bacteria is a behavior that allows prompt utilization of the substrate. The combined exoenzymatic action of a growing colony provides benefits to the individual cells when there is a rich food supply. Alternatively, an oligotrophic bacterioplankton growing slowly in a nutrient-poor environment may have a life strategy in which dispersal is promoted to optimize cell access to substrates. In the latter scenario the formation of colonies is probably not adaptive. These two different life strategies may explain the thousand-fold difference between the total number of bacteria and the number of CFU found in typical seawater samples. Over the years the discrepancy in these numbers has puzzled many authors (13). Clearly, dead and dying bacterial cells cannot form colonies; thus, the effects of virus infection and nutrient starvation have been inferred to be reasons for low viable counts (14, 19, 24). Furthermore, different states of bacterial cell physiology, such as dormancy and the so-called viable but not culturable state, have been suggested to be explanations for the lack of growth on solid media (20, 26). However, the behaviors of bacteria with different life strategies have not been considered in relation to the formation of colonies. In this study we used the dilution-to-extinction technique (6) to isolate bacterial strains unable to grow and form colonies on conventional culture media. In an attempt to understand this inability to grow and form colonies, we explored the growth behavior of three marine bacterioplankton species by using a novel assay. Bacteria were grown on seawater agar slides containing a fluorescent stain, which allowed direct observation by epifluorescence microscopy of living cells.

All of the marine bacterioplankton-derived 16S ribosomal DNA sequences previously deposited in GenBank were reanalyzed to determine the number of bacterial species in the oceanic surface waters. These sequences have been entered into the database since 1990. The rate of new additions reached a peak in 1999 and subsequently leveled off, suggesting that much of the marine microbial species richness has been sampled. When the GenBank sequences were dereplicated by using 97% similarity as a cutoff, 1,117 unique ribotypes were found. Of the unique sequences, 609 came from uncultured environmental clones and 508 came from cultured bacteria. We conclude that the apparent bacterioplankton species richness is relatively low.

To study the late β-cell-specific function of the homeodomain protein IPF1/PDX1 we have generated mice in which theIpf1/Pdx1 gene has been disrupted specifically in β cells. These mice develop diabetes with age, and we show that IPF1/PDX1 is required for maintaining the β cell identity by positively regulating insulin and islet amyloid polypeptide expression and by repressing glucagon expression. We also provide evidence that IPF1/PDX1 regulates the expression of Glut2 in a dosage-dependent manner suggesting that lowered IPF1/PDX1 activity may contribute to the development of type II diabetes by causing impaired expression of both Glut2 and insulin.