The genomic basis of trophic strategy in marine bacteria

Abstract

Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species to colonize distinct trophic habitats in the oceans. Here, we compare the genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic and oligotrophic modes of life and specifically relate the genomic features to trophic strategy for these organisms and define their molecular mechanisms of adaptation. We developed a model for predicting trophic lifestyle from genome sequence data and tested >400,000 proteins representing >500 million nucleotides of sequence data from 126 genome sequences with metagenome data of whole environmental samples. When applied to available oceanic metagenome data (e.g., the Global Ocean Survey data) the model demonstrated that oligotrophs, and not the more readily isolatable copiotrophs, dominate the ocean's free-living microbial populations. Using our model, it is now possible to define the types of bacteria that specific ocean niches are capable of sustaining.

Fig. 1.

SOM showing the two clusters of organisms used to identify markers of trophic strategy. Maps were generated and visualized with Synapse as described in Materials and Methods. The clusters show a clear delimitation between copiotrophic (blue) and oligotrophic (red) genomes. The size of each black dot is proportional to the number of genomes occupying a cell in the map.

Fig. 2.

SOMs showing five clusters of organisms with different trophic strategies. Maps were generated and visualized with Synapse as described in Materials and Methods. (Upper) Enlargement of the clustering map with positions of relevant genomes marked. Yellow, extreme oligotrophs; red, moderate oligotrophs; green and blue, moderate copiotrophs; cyan, extreme copiotrophs. (Lower) The boxes labeled “Clusters” and “Unified dist.” show the clustering and distances, respectively, with all other boxes showing the component planes. The size of each black dot is proportional to the number of genomes occupying a cell in the map. The position on the map of all of the genomes and metagenomes used is provided in Table S2.