A platform using virtual transporter proteins to simulate nutrient uptake and bacterial multispecies dynamics has been created. The purpose of this simulator is to explore the extent to which different bacterial taxa can coexist based on a mechanistic understanding of their fitness. In the simulator, taxa with different combinations of fitness traits such as the abundance of specific transporter proteins, cell size, motility, metabolic strategies, and predation are allowed to freely compete for available resources. The bacterial taxa represented in the simulator feature bacterial stereotypes at the taxonomic level of order. Metagenomic data on the taxonomic distribution of molecular transporters, from a Baltic Sea time series, provide a framework for the uptake of nutrients by the bacteria. Physical space is not explicitly simulated, so the arena in the experiment is inherently homogeneous as this appears to be a good approximation to an aquatic microbial food web. However, the simulation scenario is based on physical constraints such as the diffusion encounter of nutrients and viruses as well as swimming predators. Examples of mechanisms that are parameterized include growth rate, virus infection, and predation. The overall structure is a classical pelagic microbial food web, where protozoa graze on bacteria and algae and are in turn grazed by microzooplankton. The annual growth pattern of primary producers, and thus the input of organic material over the course of a season, is driven by the flux of light at a given latitude. The results show that the model generates a realistic annual pattern for the development of an aquatic microbial food web and that a diverse bacterial community can be maintained in the simulator over several annual cycles. Notably, the simulator generated similar bacterial population dynamics compared to in situ data.

In this study, we examined transporter genes in metagenomic and metatranscriptomic data from a time-series survey in the temperate marine environment of the Baltic Sea. We analyzed the abundance and taxonomic distribution of transporters in the 3 mu m-0.2 mu m size fraction comprising prokaryotes and some picoeukaryotes. The presence of specific transporter traits was shown to be guiding the succession of these microorganisms. A limited number of taxa were associated with the dominant transporter proteins that were identified for the nine key substrate categories for microbial growth. Throughout the year, the microbial taxa at the level of order showed highly similar patterns in terms of transporter traits. The distribution of transporters stayed the same, irrespective of the abundance of each taxon. This would suggest that the distribution pattern of transporters depends on the bacterial groups being dominant at a given time of the year. Also, we find notable numbers of secretion proteins that may allow marine bacteria to infect and kill prey organisms thus releasing nutrients. Finally, we demonstrate that transporter proteins may provide clues to the relative importance of biogeochemical processes, and we suggest that virtual transporter functionalities may become important components in future population dynamics models.</p>

Here, we examine the use of bacterial isolates growing in artificial media or seawater as a means to investigate bacterial activity in the upper ocean. The discovery of a major role of bacteria in the ocean's carbon cycle owes greatly to the development of culture-independent assemblage-level approaches; however, this should not detract from the recognition of model isolates as representing the environmental microbiome. A long-established tool for culturing bacteria, in medicine and general microbiology, has been agar plates. In addition, a great variety of liquid substrates including seawater have been used to successfully identify and cultivate important bacteria such as Pelagibacter ubique. Yet, the discrepancy between microscopic counts and plate counts, the great plate count anomaly, has led to a biased perception of the limited relevance of isolated bacteria. Linking isolates to whole-genome sequencing, phylogenetic analysis and computational modeling will result in culturable model bacteria from different habitats. Our main message is that bacterial ecophysiology, particularly growth rates in seawater, and functionalities inferred through the identity, abundance and expression of specific genes could be mechanistically linked if more work is done to isolate, culture and study bacteria in pure cultures. When we rally behind a strategy aimed at culturing targeted phenotypes, we are not saying that culture independent studies of bacteria in the sea are not informative. We are suggesting that culturebased studies can help integrate the ecological and genomic views.

Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

To obtain insights into the coupling between community composition, diversity and community function, bacterioplankton assemblages from the Gulf of Trieste (Northern Adriatic Sea) were exposed to increasing environmental stress throughout 2 wk in continuous seawater cultures to construct communities differing in composition and diversity. The assemblages were exposed to (1) decreased temperature, (2) decreased temperature and phosphate addition or (3) decreased temperature, phosphate addition and lowered oxygen level. Bacterial and viral abundances as well as bacterial community composition stabilized during the second week of the experiment. Denaturing gradient gel electrophoresis and pyrosequencing of 16S rRNA genes showed dramatic reductions in bacterial diversity in all treatments and major compositional differences relative to the inoculum. Nevertheless, no differences in the ability to exploit dissolved organic carbon (DOC) were found for the acquired communities relative to the inoculum, indicating that the bacterial communities were functionally redundant. We speculate that oscillations in exploitation of the DOC pool in situ are mainly governed by factors limiting the overall bacterial growth, rather than perturbations affecting only subsets of the microbial biota.

The atmosphere is host to an omnipresent bacterial community that may influence fundamental atmospheric processes such as cloud formation and precipitation onset. Knowledge of this bacterial community is scarce, particularly in air masses relevant to cloud formation. Using a light aircraft, we sampled above the atmospheric boundary layer-that is, at heights at which cloud condensation occurs-over coastal areas of Sweden and Denmark in summer 2009. Enumeration indicated total bacterial numbers of 4 x 10(1) to 1.8 x 10(3) m(-3) air and colony-forming units of 0-6 bacteria m(-3) air. 16S rRNA gene libraries constructed from samples collected above the Baltic Sea coast revealed a highly diverse bacterial community dominated by species belonging to the genera Sphingomonas and Pseudomonas. Bacterial species known to carry ice-nucleating proteins were found in several samples. Modeled back trajectories suggested the potential sources of the sampled bacteria to be diverse geographic regions, including both marine and terrestrial environments in the northern hemisphere. Several samples contained 16S rRNA genes from plant chloroplasts, confirming a terrestrial contribution to these samples. Interestingly, the airborne bacterial community displayed an apparent seasonal succession that we tentatively ascribe to in situ succession in the atmosphere.

A bacterial community may be resistant to environmental disturbances if some of its species show metabolic flexibility and physiological tolerance to the changing conditions. Alternatively, disturbances can change the composition of the community and thereby potentially affect ecosystem processes. The impact of disturbance on the composition of bacterioplankton communities was examined in continuous seawater cultures. Bacterial assemblages from geographically closely connected areas, the Baltic Sea (salinity 7 and high dissolved organic carbon [DOC]) and Skagerrak (salinity 28 and low DOC), were exposed to gradual opposing changes in salinity and DOC over a 3-week period such that the Baltic community was exposed to Skagerrak salinity and DOC and vice versa. Denaturing gradient gel electrophoresis and clone libraries of PCR-amplified 16S rRNA genes showed that the composition of the transplanted communities differed significantly from those held at constant salinity. Despite this, the growth yields (number of cells ml(-1)) were similar, which suggests similar levels of substrate utilization. Deep 454 pyrosequencing of 16S rRNA genes showed that the composition of the disturbed communities had changed due to the recruitment of phylotypes present in the rare biosphere of the original community. The study shows that members of the rare biosphere can become abundant in a bacterioplankton community after disturbance and that those bacteria can have important roles in maintaining ecosystem processes.

Although temperature is a key parameter controlling the activity and growth of all microorganisms, information about how water temperature may structure the bacterioplankton community is not consistent. We examined the relationship between temperature and the community composition, cell volume, and morphology of marine bacterioplankton in 4 continuous cultures harbouring multispecies communities. All 4 cultures were maintained at a turnover time of 0.04 h(-1) but at different temperatures of 10, 15, 20, and 25 degrees C. Denaturing gradient gel electrophoresis analyses showed that the community composition shifted in response to temperature. Cell volumes were determined from digital photomicrographs using an image analysis program, which also allowed the identification of 3 morphological types of bacteria: cocci-, rod-, and vibrio-shaped bacteria. Mean bacterial cell volume decreased with increasing temperature, e.g., by 39% when the temperature was increased from 10 degrees C to 20 degrees C. When the temperature increased, the bacterial morphology also shifted from dominance by rod- and vibrio-shaped bacteria to dominance by coccoid bacteria. The results clearly indicate the potential role of temperature in driving the community succession of bacterioplankton and in selecting for smaller cells at higher temperatures.

Factors influencing the production of primary marine aerosol are of great importance to better understand the marine aerosols' impact on our climate. Bubble-bursting from whitecaps is considered the most effective mechanism for sea spray production, and a way of sea-air transfer for some bacterial species. Two coastal sites in the Baltic Sea were used to investigate aerosol and bacterial emissions from the bubble-bursting process by letting a jet of water hit a water surface within an experimental tank, mimicking the actions of breaking waves. The aerosol size distribution spectra from the two sites were similar and conservative in shape where the modes were centered at about 200 nm dry diameter. We found a distinct decrease in bubbled aerosol production with increasing water temperature. A clear diurnal cycle in bubbled aerosol production was observed, anticorrelated with both water temperature and dissolved oxygen, which to our knowledge has never been shown before. A link between decreasing aerosol production in daytime and phytoplankton activity is likely to be an important factor. Colony-forming bacteria were transferred to the atmosphere via the bubble-bursting process, with a linear relationship to their seawater concentration.

Cyanobacteria are thought to be the main N(2)-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N(2) fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.