Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus
- Massachusetts Institute of Technology, United States
- Bigelow Laboratory for Ocean Sciences, United States
Abstract
Intraspecific trait variability has important consequences for the function and stability of marine ecosystems. Here we examine variation in the ability to use nitrate across hundreds of Prochlorococcus genomes to better understand the modes of evolution influencing intraspecific allocation of ecologically important functions. Nitrate assimilation genes are absent in basal lineages but occur at an intermediate frequency that is randomly distributed within recently emerged clades. The distribution of nitrate assimilation genes within clades appears largely governed by vertical inheritance, gene loss, and homologous recombination. By mapping this process onto a model of Prochlorococcus' macroevolution, we propose that niche-constructing adaptive radiations and subsequent niche partitioning set the stage for loss of nitrate assimilation genes from basal lineages as they specialized to lower light levels. Retention of these genes in recently emerged lineages has likely been facilitated by selection as they sequentially partitioned into niches where nitrate assimilation conferred a fitness benefit.
Data availability
Sequencing data have been deposited in Integrated Microbial Genomes under the accession numbers (IMG Genome ID) 2681812899, 2681812900, 2681812901, and 2681812859.All data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for Figure 1, Figure 2, Figure 3, Figure 6, Figure 7, Table 1, Table 2, Table 3, Table 4, and Table 5.
Article and author information
Author details
Funding
National Science Foundation (OCE-1153588)
- Sallie W Chisholm
National Science Foundation (DBI-0424599)
- Sallie W Chisholm
National Science Foundation (OCE-1335810)
- Ramunas Stepanauskas
Simons Foundation (337262)
- Sallie W Chisholm
Simons Foundation (329108)
- Sallie W Chisholm
Gordon and Betty Moore Foundation (GBMF495)
- Sallie W Chisholm
Gordon and Betty Moore Foundation (GBMF4511)
- Sallie W Chisholm
Simons Foundation (509034SCFY17)
- Sallie W Chisholm
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Paul G Falkowski, Rutgers University, United States
Version history
- Received: August 13, 2018
- Accepted: January 31, 2019
- Accepted Manuscript published: February 1, 2019 (version 1)
- Version of Record published: February 11, 2019 (version 2)
Copyright
© 2019, Berube et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus
eLife 8:e41043.
https://doi.org/10.7554/eLife.41043
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