Nutrient uptake by oceanic oligotrophic bacteria

Abstract

The oligotrophic ubiquitous SAR11 clade of alphaproteobacteria and Prochlorococcus cyanobacteria numerically dominate bacterioplankton that drives the ecosystems of the five subtropical oceanic gyres, which cumulatively cover 40% of earth. Common gyre features like extremely low nutrient and chlorophyll concentrations as well as dominance of obligate oligotrophs suggest that the gyre ecosystems are uniform and function at the same pace. Competition in oligotrophic environment should favour optimisation of surface to volume ratio and selection for efficient high affinity transporters, which could be structurally divergent from known transport systems.

To test the hypothesis of gyre ecosystem similarity, SAR11 abundance and metabolic rates (used as a proxy for growth) were compared between three oceanic gyres by assessing their in situ uptake rates of amino acids: leucine and methionine (chapter 3). Bacterial abundance as well as absolute SAR11 amino acid uptake rates were higher in more productive waters of the Equatorial convergence zone of the Atlantic Ocean and SAR11 abundance in the surface mixed layer were similar in the three studied gyres, supporting the similarity hypothesis. However, SAR11 cells took up amino acids 3 – 4 times slower in the South Pacific gyre than in the North and South Atlantic gyres, despite similar concentrations of the amino acids in the gyres. Evidently SAR11 concentration similarity conceals metabolic differences, which should better reflect contrasts in the gyre environments of the two oceans. Thus, the SAR11 metabolic rates indicate that the microbe-driven gyre ecosystem of the South Pacific could function one third slower than the analogous ecosystems of the Atlantic.

Being able to dominate bacterioplankton while competing for nutrients at nanomolar concentrations, oligotrophs might possess uniquely efficient uptake systems. Identification of porins and high affinity ABC transporters in available genomes was guided by bioinformatical analysis (chapter 4), showing great diversity. Identified porins as well as phosphate-(PstS) and iron-binding proteins (FutA) of Prochlorococcus, which are responsible for the respective transporters affinity, were chosen for analysis using X-ray crystallography (chapter 5, 6 and 7). In silico analysis of porin models revealed unique features, which might influence transport function in vivo. High resolution structures of PstS and FutA were determined, enabling a thorough comparison to other substrate-binding proteins such as FutA from Trichodesmium. Interestingly, there is little variation in overall ligand coordination. However, small structural differences might hint at differences in ligand binding. Analysis of the binding site of FutA shows unexpected iron-binding plasticity in the determined crystal structures, which might have implications for iron acquisition in vivo. Employing a combination of UV-Vis spectroscopy and multi-crystal merging techniques made it possible to monitor X-ray induced site specific radiation damage on the iron centre of FutA (chapter 8). The dose of the multi-crystal FutA structure is possibly the lowest reported X-ray dose, to our knowledge, for a crystal structure determined using non-XFEL methods, enabling us to study the iron-binding site mostly unaffected by radiation damage and X-ray induced artefacts.

In conclusion, this work was aimed to unveil unique adaptations of the most abundant organisms on earth. The employed multi-disciplinary approach led to discoveries with implications for diverse ecological and structural investigations.

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ORCID for Ivo Tews: orcid.org/0000-0002-4704-1139

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