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- Alonso-Saez, Laura, et al.
(författare)
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Factors controlling the year-round variability in carbon flux through bacteria in a coastal marine system
- 2008
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Ingår i: Ecosystems (New York. Print). - : Springer Science and Business Media LLC. - 1432-9840 .- 1435-0629. ; 11:3, s. 397-409
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Tidskriftsartikel (refereegranskat)abstract
- Data from several years of monthly samplings are combined with a 1-year detailed study of carbon flux through bacteria at a NW Mediterranean coastal site to delineate the bacterial role in carbon use and to assess whether environmental factors or bacterial assemblage composition affected the in situ rates of bacterial carbon processing. Leucine (Leu) uptake rates [as an estimate of bacterial heterotrophic production (BHP)] showed high interannual variability but, on average, lower values were found in winter (around 50 pM Leu(-1) h(-1)) as compared to summer (around 150 pM Leu(-1) h(-1)). Leu-to-carbon conversion factors ranged from 0.9 to 3.6 kgC mol Leu(-1), with generally higher values in winter. Leu uptake was only weakly correlated to temperature, and over a full-year cycle (in 2003), Leu uptake peaked concomitantly with winter chlorophyll a (Chl a) maxima, and in periods of high ectoenzyme activities in spring and summer. This suggests that both low molecular weight dissolved organic matter (DOM) released by phytoplankton, and high molecular weight DOM in periods of low Chl a, can enhance BHP. Bacterial respiration (BR, range 7-48 mu g C l(-1) d(-1)) was not correlated to BHP or temperature, but was significantly correlated to DOC concentration. Total bacterial carbon demand (BHP plus BR) was only met by dissolved organic carbon produced by phytoplankton during the winter period. We measured bacterial growth efficiencies by the short-term and the long-term methods and they ranged from 3 to 42%, increasing during the phytoplankton blooms in winter (during the Chl a peaks), and in spring. Changes in bacterioplankton assemblage structure (as depicted by denaturing gradient gel electrophoresis fingerprinting) were not coupled to changes in ecosystem functioning, at least in bacterial carbon use.
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- Gasol, Josep M., et al.
(författare)
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Towards a better understanding of microbial carbon flux in the sea
- 2008
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Ingår i: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 53:1, s. 21-38
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Tidskriftsartikel (refereegranskat)abstract
- We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.
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- 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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- Gourdon, Pontus Emanuel, 1978, et al.
(författare)
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Optimized in vitro and in vivo expression of proteorhodopsin: A seven-transmembrane proton pump
- 2008
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Ingår i: Protein Expression and Purification. - : Elsevier BV. - 1096-0279 .- 1046-5928. ; 58:1, s. 103-113
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Tidskriftsartikel (refereegranskat)abstract
- Proteorhodopsin is an integral membrane light-harvesting proton pump that is found in bacteria distributed throughout global surface waters. Here, we present a protocol for functional in vitro production of pR using a commercial cell-free synthesis system yielding 1.0 mg purified protein per milliliter of cell lysate. We also present an optimized protocol for in vivo over-expression of pR in Escherichia coli, and a two-step purification yielding 5 mg of essentially pure functional protein per liter of culture. Both approaches are straightforward, rapid, and easily scalable. Thus either may facilitate the exploitation of pR for commercial biotechnological applications. Finally, the implications of some observations of the in vitro synthesis behavior, as well as preliminary results towards a structural determination of pR are discussed.
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