| 1. |
- Gonzalez, J. M., et al.
(författare)
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Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)
- 2008
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 105:25, s. 8724-8729
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhoclopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhoclopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.
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| 2. |
- González, J. M., et al.
(författare)
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Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134
- 2011
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Ingår i: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 77:24, s. 8676-8686
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhodopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhodopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.
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| 3. |
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| 4. |
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| 5. |
- Fahlgren, Camilla, et al.
(författare)
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Seawater mesocosm experiments in the Arctic uncover differential transfer of marine bacteria to aerosols
- 2015
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229 .- 1758-2229. ; 7:3, s. 460-470
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Tidskriftsartikel (refereegranskat)abstract
- Biogenic aerosols critically control atmospheric processes. However, although bacteria constitute major portions of living matter in seawater, bacterial aerosolization from oceanic surface layers remains poorly understood. We analysed bacterial diversity in seawater and experimentally generated aerosols from three Kongsfjorden sites, Svalbard. Construction of 16S rRNA gene clone libraries from paired seawater and aerosol samples resulted in 1294 sequences clustering into 149 bacterial and 34 phytoplankton operational taxonomic units (OTUs). Bacterial communities in aerosols differed greatly from correspondingseawater communities in three out of four experiments. Dominant populations of both seawater and aerosols were Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria. Across the entire dataset, most OTUs from seawater could also be found in aerosols; in each experiment, however, several OTUs were either selectively enriched in aerosols or little aerosolized. Notably, a SAR11 clade OTU was consistently abundant in the seawater, but was recorded insignificantly lower proportions in aerosols. A strikingly high proportion of colony-forming bacteria were pigmented in aerosols compared with seawater, suggesting that selection during aerosolization contributes to explaining elevated proportions of pigmented bacteria frequently observed in atmospheric samples. Our findings imply that atmospheric processes could be considerably influenced by spatiotemporal variations in the aerosolization efficiency of different marine bacteria.
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| 6. |
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| 7. |
- Gómez-Consarnau, Laura, et al.
(författare)
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Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation
- 2010
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Ingår i: PLoS biology. - : Public Library Science. - 1544-9173 .- 1545-7885. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean. Although their function as proton pumps with energy-yielding potential has been demonstrated, the ecological role of proteorhodopsins remains largely unexplored. Here, we report the presence and function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio strain AND4 obtained proteorhodopsin through lateral gene transfer, which could have modified the ecology of this marine bacterium. We demonstrate an increased long-term survival of AND4 when starved in seawater exposed to light rather than held in darkness. Furthermore, mutational analysis provides the first direct evidence, to our knowledge, linking the proteorhodopsin gene and its biological function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness advantage to marine bacteria, representing a novel mechanism for bacterioplankton to endure frequent periods of resource deprivation at the ocean’s surface.
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| 8. |
- Gómez-Consarnau, Laura, et al.
(författare)
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Structuring of bacterioplankton communities by specific dissolved organic carbon compounds
- 2012
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Ingår i: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 14:9, s. 2361-2378
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Tidskriftsartikel (refereegranskat)abstract
- The main role of microorganisms in the cycling of the bulk dissolved organic carbon pool in the ocean is well established. Nevertheless, it remains unclear if particular bacteria preferentially utilize specific carbon compounds and whether such compounds have the potential to shape bacterial community composition. Enrichment experiments in the Mediterranean Sea, Baltic Sea and the North Sea (Skagerrak) showed that different low-molecular-weight organic compounds, with a proven importance for the growth of marine bacteria (e.g. amino acids, glucose, dimethylsulphoniopropionate, acetate or pyruvate), in most cases differentially stimulated bacterial growth. Denaturing gradient gel electrophoresis fingerprints and 16S rRNA gene sequencing revealed that some bacterial phylotypes that became abundant were highly specific to enrichment with specific carbon compounds (e.g. Acinetobacter sp. B1-A3 with acetate or Psychromonas sp. B3-U1 with glucose). In contrast, other phylotypes increased in relative abundance in response to enrichment with several, or all, of the investigated carbon compounds (e.g. Neptuniibacter sp. M2-A4 with acetate, pyruvate and dimethylsulphoniopropionate, and Thalassobacter sp. M3-A3 with pyruvate and amino acids). Furthermore, different carbon compounds triggered the development of unique combinations of dominant phylotypes in several of the experiments. These results suggest that bacteria differ substantially in their abilities to utilize specific carbon compounds, with some bacteria being specialists and others having a more generalist strategy. Thus, changes in the supply or composition of the dissolved organic carbon pool can act as selective forces structuring bacterioplankton communities.
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| 9. |
- Hultin, Kim, et al.
(författare)
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Aerosol and bacterial emissions from Baltic Seawater
- 2011
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Ingår i: Atmospheric research. - : Elsevier BV. - 0169-8095 .- 1873-2895. ; 99:1, s. 1-14
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 10. |
- Lekunberri, Itziar, et al.
(författare)
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The phylogenetic and ecological context of cultured and whole genome-sequenced planktonic bacteria from the coastal NW Mediterranean Sea
- 2014
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020 .- 1618-0984. ; 37:3, s. 216-228
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Tidskriftsartikel (refereegranskat)abstract
- Microbial isolates are useful models for physiological and ecological studies and can also be used to reassemble genomes from metagenomic analyses. However, the phylogenetic diversity that can be found among cultured marine bacteria may vary significantly depending on the isolation. Therefore, this study describes a set of 136 bacterial isolates obtained by traditional isolation techniques from the Blanes Bay Microbial Observatory, of which seven strains have had the whole genome sequenced. The complete set was compared to a series of environmental sequences obtained by culture-independent techniques (60 DGGE sequences and 303 clone library sequences) previously obtained by molecular methods. In this way, each isolate was placed in both its "ecological" (time of year, nutrient limitation, chlorophyll and temperature values) context or setting, and its "phylogenetic" landscape (i.e. similar organisms that were found by culture-independent techniques, when they were relevant, and when they appeared). Nearly all isolates belonged to the Gammaproteobacteria, Alphaproteobacteria, or the Bacteroidetes (70, 40 and 20 isolates, respectively). Rarefaction analyses showed similar diversity patterns for sequences from isolates and molecular approaches, except for Alphaproteobacteria where cultivation retrieved a higher diversity per unit effort. Approximately 30% of the environmental clones and isolates formed microdiversity clusters constrained at 99% 16S rRNA gene sequence identity, but the pattern was different in Bacteroidetes (less microdiversity) than in the other main groups. Seventeen cases (12.5%) of nearly complete (98-100%) rRNA sequence identity between isolates and environmental sequences were found: nine in the Alphaproteobacteria, five in the Gammaproteobacteria, and three in the Bacteroidetes, indicating that cultivation could be used to obtain at least some organisms representative of the various taxa detected by molecular methods. Collectively, these results illustrated the largely unexplored potential of culturing on standard media for complementing the study of microbial diversity by culture-independent techniques and for obtaining phylogenetically distinct model organisms from natural seawater.
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