Uptake of Prochlorococcus-derived metabolites by Alteromonas macleodii MIT1002 shows high levels of substrate specificity

Seawater contains an abundance of small biomolecules, or metabolites, that are highly labile components of dissolved organic matter (DOM). Marine microbes interact by exchanging metabolites, thus shaping marine microbial ecology, DOM composition, and global carbon cycling. To better constrain one set of microbe-metabolite interactions, we cultured the marine gammaproteobacterium Alteromonas macleodii MIT1002 on a range of compounds excreted by a sympatric cyanobacterium, Prochlorococcus. Alteromonas could assimilate the branched chain amino acids leucine, isoleucine, and valine, as well as 3-methyl-2-oxobutanoic acid (a branched chain ketoacid intermediate of valine metabolism), but not thymidine, kynurenine, 4-hydroxybenzoic acid, or the other branched chain ketoacids. The assimilation of branched chain amino acids indicates that Alteromonas can metabolically process each corresponding ketoacid, suggesting that transporter specificity underlies the observed substrate specificity for 3-methyl-2-oxobutanoic acid. These experiments show that even subtle changes in chemical structure can result in different microbial interactions and different fates for dissolved metabolites. Significance StatementMicrobial interactions with dissolved organic matter are important controls on the marine carbon cycle. Dissolved organic matter is often considered in bulk, which leaves the specificity and nature of these interactions poorly constrained. Here we show that microbe-molecule interactions can be highly specific, distinguishing between molecules that are structurally and biochemically similar. This implies that small changes in this pool of carbon could have large impacts for the overall system function, and that measuring this pool of carbon with molecular-level resolution is important to characterizing microbe-molecule interactions. We further explore the mechanism underlying the observed substrate specificity and suggest that it is caused by transporter selectivity, meaning the ability of these microbes to selectively uptake specific dissolved organic molecules.