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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.

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.

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.

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 worldwide 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.

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.

Bubbles bursting from whitecaps are considered to be the most effective mechanism for particulate matter to be ejected into the atmosphere from the Earth's oceans. To realistically predict the climate effect of marine aerosols, global climate models require process-based understanding of particle formation from bubble bursting. During a cruise on the highly biologically active waters of the northeastern Atlantic Ocean in the summer of 2006, the submicrometer primary marine aerosol produced by a jet of seawater impinging on a seawater surface was investigated. The produced aerosol size spectra were centered on 200 nm in dry diameter and were conservative in shape throughout the cruise. The aerosol number production was negatively correlated with dissolved oxygen (DO) in the water (r < −0.6 for particles of dry diameter Dp > 200 nm). An increased surfactant concentration as a result of biological activity affecting the oxygen saturation is thought to diminish the particle production. The lack of influence of chlorophyll on aerosol production indicates that hydrocarbons produced directly by the photosynthesis are not essential for sea spray production. The upward mixing of deeper ocean water as a result of higher wind speed appears to affect the aerosol particle production, making wind speed influence aerosol production in more ways than by increasing the amount of whitecaps. The bubble spectra produced by the jet of seawater was representative of breaking waves at open sea, and the particle number production was positively correlated with increasing bubble number concentration with a peak production of 40–50 particles per bubble.

The presence of bacteria in aerosols has been known for centuries, but information on their identity and role in dispersing microbial traits is still limited. This study monitored the airborne bacterial community during an annual survey using samples collected from a 25-m tower near the Baltic Sea coast. The number of CFU was estimated using agar plates while the most probable number (MPN) of viable bacteria was estimated using dilution-to-extinction culturing assays (DCAs). The MPN and CFU values produced quantitatively similar results, displaying a pronounced seasonal pattern, with the highest numbers in winter. The most dominant bacteria growing in the DCAs all formed colonies on agar plates, were mostly pigmented (80%), and closely resembled (>97%) previously cultured bacteria based on their 16S rRNA gene sequences. 16S rRNA gene clone libraries were constructed on eight occasions during the survey; these revealed a highly diverse community with a few abundant operational taxonomic units (OTUs) and a long tail of rare OTUs. A majority of the cloned sequences (60%) were also most closely related to previously ""cultured"" bacteria. Thus, both culture-dependent and culture-independent techniques indicated that bacteria able to form colonies on agar plates predominate in the atmosphere. Both the DCAs and clone libraries indicated the dominance of bacteria belonging to the genera Sphingomonas sp. and Pseudomonas sp. on several sampling occasions. Potentially pathogenic strains as well as sequences closely resembling bacteria known to act as ice nuclei were found using both approaches. The origin of the sampled air mass was estimated using backward trajectories, indicating a predominant marine source., authorCount :4

The episodic hyperproduction of mucilage macroaggregates in the northern Adriatic Sea creates an important site for the accumulation, transformation, and degradation of organic matter. In this review, the structure and function of macroaggregate components in relation to their macrogel and colloidal fractions are discussed. High resolution electron microscopy showed a very complex structure, a honeycomb-like structure of the mucus macroagregates that might grow to macroscopic sizes. The process of the formation and microbial interaction with the physicochemical diversity of the organic matter pool is poorly understood. Whether the in situ bacteria react to the carbohydrate-rich mucus as an imbalance in its C:N:P ratio or whether the mucus is in fact largely a bacterial construct in relation to high dissolved organic carbon levels is unknown. The majority of carbohydrate and protein macroaggregate pools are potentially degradable, while the great majority of lipids can be preserved in the water column and exported away or finally deposited on the seabed. Our present knowledge indicates that different macroaggregate fractions and components are subjected to compositional selective reactivity, with important implications for macroaggregate persistence. Future work should reconcile the discrepancies between bacterial ectoenzyme potential activities and biogeochemical degradation sequences based on actual measurements. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies, has profound implications for the function of these complex communities. We need to improve our understanding of the dynamic relationship among bacteria, other microorganisms, and a variety of organic matter forms.

Flavobacteria are emerging as an important group of organisms associated with the degradation of complex organic matter in aquatic environments. A novel Gram-reaction-negative, heterotrophic, rod-shaped, aerobic, yellow-pigmented and gliding bacterium, strain SCB36(T), was isolated from a protein-enriched seawater sample, collected at Scripps Pier, Southern California Bight (Eastern Pacific). Analysis of the 16S rRNA gene sequence showed that the bacterium was related to members of the genus Winogradskyella within the family Flavobacteriaceae, phylum Bacteroidetes. 16S rRNA gene sequence similarity to the other Winogradskyella species was 94.5-97.1%. DNA-DNA relatedness between strain SCB36(T) and Winogradskyella thalassocola KMM 3907(T), its closest relative in terms of 16S rRNA gene sequence similarity, was 20%. On the basis of the phylogenetic and phenotypic data, strain SCB36(T) represents a novel species of the genus Winogradskyella, for which the name Winogradskyella rapida sp. nov. is proposed. The type strain is SCB36(T) (=CECT 7392(T) =CCUG 56098(T)).

Marine bacteria can cause harm to single-celled and multicellular eukaryotes. However, relatively little is known about the underlying genetic basis for marine bacterial interactions with higher organisms. We examined whole-genome sequences from a large number of marine bacteria for the prevalence of homologues to virulence genes and pathogenicity islands known from bacteria that are pathogenic to terrestrial animals and plants. As many as 60 out of 119 genomes of marine bacteria, with no known association to infectious disease, harboured genes of virulence-associated types III, IV, V and VI protein secretion systems. Type III secretion was relatively uncommon, while type IV was widespread among alphaproteobacteria (particularly among roseobacters) and type VI was primarily found among gammaproteobacteria. Other examples included homologues of the Yersinia murine toxin and a phage-related 'antifeeding' island. Analysis of the Global Ocean Sampling metagenomic data indicated that virulence genes were present in up to 8% of the planktonic bacteria, with highest values in productive waters. From a marine ecology perspective, expression of these widely distributed genes would indicate that some bacteria infect or even consume live cells, that is, generate a previously unrecognized flow of organic matter and nutrients directly from eukaryotes to bacteria.

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.