Genomic-assisted determination of the natural nutrient requirements of the cosmopolitan marine bacterium 'Candidatus Pelagibacter ubique' Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/s4655j96c

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  • To identify factors limiting 'Candidatus Pelagibacter ubique' maximum cell density and growth rate in pure culture on seawater, the genome sequence of 'Cand. P. ubique' was analyzed, culturing experiments with organic and inorganic nutrient additions were made, and radiotracer uptake experiments were performed. The genome was sequenced, custom data mining tools were developed, and all major biosynthetic and energy pathways were reconstructed from a genome annotation. Analysis of the genomic data suggested 'Cand. P. ubique' might be limited by the availability of reduced sulfur, since genes cysDNCHIJ, used for assimilatory sulfate reduction, were missing. When reduced sulfur in the form of 3-dimethylsulfoniopropionate (DMSP), methionine, or cysteine was added to filtered, autoclaved seawater containing all other nutrients in excess, maximum cell yield increased an order of magnitude. But, increasing DMSP additions from 50 nM to 10 μM did not lead to higher cell densities at a normal growth rate; instead, cultures increased in cell density from 3.03 x 10⁶ cells ml⁻¹ to 2.1 x 10⁷ cells ml⁻¹, at a growth rate of 0.110 d⁻¹ instead of 0.664 d⁻¹. An additional hypothesis was that, due to the inefficiency with which threonine degradation to glycine compensates for missing serBC genes, and the presence of a glycine-activated riboswitch on malate synthase, the growth rate using DMSP as a sole sulfur source would be improved by addition of glycine betaine because glycine can be used as a methyl acceptor to regenerate methyl carriers needed to demethylate DMSP. When glycine betaine was added to filtered, autoclaved seawater containing DMSP and all other nutrients in excess, growth rate increased.
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