Abstract
Prochlorococcus contributes significantly to ocean primary productivity. The link between primary productivity and iron in specific ocean regions is well established and iron limitation of Prochlorococcus cell division rates in these regions has been shown. However, the extent of ecotypic variation in iron metabolism among Prochlorococcus and the molecular basis for differences is not understood. Here, we examine the growth and transcriptional response of Prochlorococcus strains, MED4 and MIT9313, to changing iron concentrations. During steady state, MIT9313 sustains growth at an order-of-magnitude lower iron concentration than MED4. To explore this difference, we measured the whole-genome transcriptional response of each strain to abrupt iron starvation and rescue. Only four of the 1159 orthologs of MED4 and MIT9313 were differentially expressed in response to iron in both strains. However, in each strain, the expression of over a hundred additional genes changed, many of which are in labile genomic regions, suggesting a role for lateral gene transfer in establishing diversity of iron metabolism among Prochlorococcus. Furthermore, we found that MED4 lacks three genes near the iron-deficiency-induced gene (idiA) that are present and induced by iron stress in MIT9313. These genes are interesting targets for studying the adaptation of natural Prochlorococcus assemblages to local iron conditions as they show more diversity than other genomic regions in environmental metagenomic databases.
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Acknowledgements
We acknowledge Debbie Lindell and the G Church Lab for the design of the MD4-9313 array and thank Claudia Steglich, Maureen Coleman, Daniel Sher, Paul Berube, Tyler Goepfert and Erin Bertrand for their involvement in pilot experiments, growth studies, array analysis and interpretation of results. We are also very grateful to Eric Webb for his advice and consult on this project. Funding was provided through the Gordon and Betty Moore Foundation, NSF Biological Oceanography, NSF—CMORE and DOE—GTL to SWC. Additional funding was provided through an ONR Young Investigator Award, NSF Chemical Oceanography and NSF Environmental Genomics grants to MAS. We also thank four anonymous reviewers for their insightful comments.
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AWT, SWC and MAS designed experiments; AWT conducted experiments; AWT and KH analyzed data; KH provided computational tools and environmental metagenomic analysis; and AWT, SWC and MAS wrote the paper.
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Thompson, A., Huang, K., Saito, M. et al. Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability. ISME J 5, 1580–1594 (2011). https://doi.org/10.1038/ismej.2011.49
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DOI: https://doi.org/10.1038/ismej.2011.49
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