Ecosystem-specific selection pressures revealed through comparative population genomics

Abstract

Bacterial populations harbor vast genetic diversity that is continually shaped by abiotic and biotic selective pressures, as well as by neutral processes. Individuals coexisting in the same geographically defined population often have significantly different gene content, but whether this variation is largely adaptive or neutral remains poorly understood. Here we quantify heterogeneity in gene content for two model marine microbes, Prochlorococcus and Pelagibacter, within and between populations in the Atlantic and Pacific Oceans, to begin to understand the selective pressures that are shaping these "population genomes." We discovered a large fraction of genes that are rare in each population, reflecting continual gene transfer and loss. Despite this high variation within each population, only a few genes significantly differ in abundance between the two biogeochemically distinct environments; nearly all of these are related to phosphorus acquisition and are enriched in the Atlantic relative to the Pacific. Moreover, P-related genes from the two sites form phylogenetically distinct clusters, whereas housekeeping genes do not, consistent with a recent spread of adaptive P-related genes in the Atlantic populations. These findings implicate phosphorus availability as the dominant selective force driving divergence between these populations, and demonstrate the promise of this approach for revealing selective agents in more complex microbial systems.

Fig. 1.

Distribution of core and flexible genes (21) among Prochlorococcus populations at HOT (A) and at BATS (B). Core genes are defined as present in all 12 sequenced cultured isolates of Prochlorococcus, and the tight single-peaked distribution around the mean implies that they also are core genes and are present in one-to-one stoichiometry in these wild populations. Most flexible genes (those present in some, but not all, genomes of cultured isolates) are rare in these populations, being present in only a small proportion of the cells. The copy number per cell for each gene was estimated as described in Materials and Methods.

Fig. 2.

Relative gene frequency among Prochlorococcus and Pelagibacter populations in the oligotrophic North Pacific (HOT) and North Atlantic (BATS) subtropical ocean gyres. (A) Detection of each Prochlorococcus gene at HOT and BATS, measured as the number of pyrosequencing reads. For each gene, the number of reads detected is proportional to the product of gene length and gene multiplicity per cell. Thus, assuming similar gene lengths at both sites, genes that fall along the diagonal trend have the same relative frequency at both sites, whereas those that fall above or below the diagonal are enriched at one site compared with the other. Squares represent significantly different frequencies between sites (G test; P < 0.01); circles represent nonsignificant differences. Colored squares represent genes whose chromosomal positions are depicted in B. (B) Genome comparison of two cultured isolates of Prochlorococcus (MED4 and MIT9301), with gray lines connecting homologous genes. Genes represented by corresponding colored squares in A are clustered together in a few distinct regions of the chromosome, including hypervariable genomic islands, in these isolates. Genes marked with an asterisk are up-regulated in response to P starvation (ref. and Fig. S2). MED4 and MIT9301, isolated from the Mediterranean and the North Atlantic, respectively, are depicted because they carry the largest complements of phosphorus uptake genes among Prochlorococcus isolates (22). (C) Relative frequency of each Pelagibacter gene at HOT and BATS, as in A. (D) Genome comparison of two Pelagibacter strains, HTCC7211 and HTCC1062, as in B.

Fig. 3.

Three examples of phylogenetic patterns observed in Prochlorococcus and Pelagibacter genes, from shotgun sequences sampled at HOT (orange leaf coloring) and BATS (blue leaf coloring). (A and B) pntA, a housekeeping gene found in similar abundance at HOT and at BATS, is not phylogenetically distinct between the sites. (C and D) pstB, a gene involved in phosphate transport, is phylogenetically distinct between the two sites, reflecting recent recombination and/or selection. (E and F) fur, a gene involved in regulation of iron metabolism, is not phylogenetically distinct between the sites. For clarity, sequence identifiers have been omitted except in the case of cultured isolates.