Minimal cobalt metabolism in the marine cyanobacterium Prochlorococcus

Abstract

Despite very low concentrations of cobalt in marine waters, cyanobacteria in the genus Prochlorococcus retain the genetic machinery for the synthesis and use of cobalt-bearing cofactors (cobalamins) in their genomes. We explore cobalt metabolism in a Prochlorococcus isolate from the equatorial Pacific Ocean (strain MIT9215) through a series of growth experiments under iron- and cobalt-limiting conditions. Metal uptake rates, quantitative proteomic measurements of cobalamin-dependent enzymes, and theoretical calculations all indicate that Prochlorococcus MIT9215 can sustain growth with less than 50 cobalt atoms per cell, ∼100-fold lower than minimum iron requirements for these cells (∼5,100 atoms per cell). Quantitative descriptions of Prochlorococcus cobalt limitation are used to interpret the cobalt distribution in the equatorial Pacific Ocean, where surface concentrations are among the lowest measured globally but Prochlorococcus biomass is high. A low minimum cobalt quota ensures that other nutrients, notably iron, will be exhausted before cobalt can be fully depleted, helping to explain the persistence of cobalt-dependent metabolism in marine cyanobacteria.

Keywords: Pacific Ocean; Prochlorococcus; iron; nutrient limitation; vitamin B12.

Fig. 1.

Growth experiments with Prochlorococcus MIT9215, originally isolated from the equatorial Pacific Ocean. (A) The exponential growth rate of Prochlorococcus MIT9215 as a function of iron (white) and cobalt (blue) concentrations (calculated as the sum of inorganic metal species, Fe′ and Co′, in equilibrium with ethylenediaminetetraacetic acid [EDTA]; see Methods). (B) Dependence of specific growth rate on acquired Fe and Co (i.e., the cell quota), measured by ICP-MS. Lines show best fit curves for Eq. 1 and derived values of the minimum cell quota, q_min (R² = 0.96 for both elements). (C) Cell quotas (±1 SD) of cobalt, the cobalamin-dependent ribonucleotide reductase (NrdJ, blue), and the cobalamin-dependent methionine synthase (MetH, pink). Proteins were quantified by selected reaction monitoring of four tryptic peptides (colored bars) in large volume cultures of cobalt-limited Prochlorococcus MIT9215 (μ = 0.20 d⁻¹; SI Appendix, Table S7). Gray lines show predicted levels of these enzymes needed to support maximum growth rates (0.6 d⁻¹) observed in these experiments via use efficiency calculations (SI Appendix, Table S4).

Fig. 2.

The distribution of dissolved cobalt, dCo, in the equatorial Pacific Ocean. (A) Station locations (pink circles) from the Metzyme expedition (KM1128) relative to low-oxygen water masses originating on the Peruvian and Mexican margins. Contours mark 25-μM intervals in dissolved oxygen (O₂) between 25 μM and 100 μM at 200-m depth from the World Ocean Circulation Experiment (WOCE) gridded atlas (82). Blue shading highlights low dissolved oxygen. (B) A latitudinal section of dissolved oxygen concentrations from the Metzyme expedition. (C) dCo (operationally defined as the concentration passing through a 0.2-μm filter) and (D) dissolved phosphate (PO₄) along the same section. (E) The full depth distribution of dCo overlain with dissolved oxygen contours at 25-μM intervals between 0 and 100 μM O₂, which highlight their correlation throughout the water column (SI Appendix, Fig. S3).

Fig. 3.

Cobalt and phosphate profiles in the South Pacific Ocean from the Metzyme expedition. Removal of (A) dCo and (B) dissolved phosphate in the surface ocean is matched by surface maxima of (C) particulate cobalt and (D) particulate phosphorus. For A–D, colors and shapes indicate station locations. (E) The ratio of cobalt to phosphorus in the euphotic zone (0 to 100 m) along the Metzyme transect in both dissolved (pink) and particulate (blue) phases. Dotted black lines indicate the Co:P composition of cobalt-limited Prochlorococcus MIT9215 biomass at threshold growth rates of 0% and 95% μ_max via Eq. 1 (SI Appendix, Table S1).

Fig. 4.

Global analysis of cobalt depletion in the marine habitat of Prochlorococcus, defined as waters with temperature >12 °C. Colors represent the relative pixel density of modeled stoichiometry of total Co:PO₄ and Fe:PO₄ (the sum of dissolved and particulate phases) in the surface ocean, with pink colors indicating a large number of pixels (i.e., model grid cells). Crosses indicate measurements of dissolved Co, Fe, and PO₄ from the GEOTRACES Intermediate Data Product 2017 (65) from the surface mixed layer (0 to 30 m). Minimum Co and Fe requirements of Prochlorococcus MIT9215 are used to define growth limitation domains for Co and Fe (solid black lines). Dashed lines mark the shift in nutrient limitation domains if cobalt requirements increase by 10-fold (a Co:P ratio of 260 × 10⁻⁶ at 95% μ_max), which corresponds to Co:P ratios of E. huxleyi cultures grown in low-Zn media (67).