Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes


Surface ocean waters are dominated by planktonic bacterial lineages with highly reduced genomes. The best examples are the cyanobacterial genus Prochlorococcus, the alphaproteobacterial clade SAR11 and the gammaproteobacterial clade SAR86, which together represent over 50% of the cells in surface oceans. Several studies have identified signatures of selection on these lineages in today's ocean and have postulated selection as the primary force throughout their evolutionary history. However, massive loss of genomic DNA in these lineages often occurred in the distant past, and the selective pressures underlying these ancient events have not been assessed. Here, we probe ancient selective pressures by computing %GC-corrected rates of conservative and radical nonsynonymous nucleotide substitutions. Surprisingly, we found an excess of radical changes in several of these lineages in comparison to their relatives with larger genomes. Furthermore, analyses of allelic genome sequences of several populations within these lineages consistently supported that radical replacements are more likely to be deleterious than conservative changes. Our results suggest coincidence of massive genomic DNA losses and increased power of genetic drift, but we also suggest that additional evidence independent of the nucleotide substitution analyses is needed to support a primary role of genetic drift driving ancient genome reduction of marine bacterioplankton lineages.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Analysis of conservative and radical nonsynonymous nucleotide substitution among Prochlorococcus lineages.
Figure 2: Analysis of conservative and radical nonsynonymous nucleotide substitution between SAR86 and other Gammaproteobacterial lineages.
Figure 3: Analysis of conservative and radical nonsynonymous nucleotide substitution between SAG-O19 and other Roseobacter lineages.
Figure 4: Analysis of conservative and radical nonsynonymous nucleotide substitution between SAR11 and other Alphaproteobacterial lineages.


  1. 1

    Giovannoni, S. J., Thrash, J. C. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553–1565 (2014).

    Article  Google Scholar 

  2. 2

    Swan, B. K. et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proc. Natl Acad. Sci. USA 110, 11463–11468 (2013).

    CAS  Article  Google Scholar 

  3. 3

    Dufresne, A., Garczarek, L. & Partensky, F. Accelerated evolution associated with genome reduction in a free-living prokaryote. Genome Biol. 6, R14 (2005).

    Article  Google Scholar 

  4. 4

    Viklund, J., Ettema, T. J. G. & Andersson, S. G. E. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 29, 599–615 (2012).

    CAS  Article  Google Scholar 

  5. 5

    Batut, B., Knibbe, C., Marais, G. & Daubin, V. Reductive genome evolution at both ends of the bacterial population size spectrum. Nat. Rev. Microbiol. 12, 841–850 (2014).

    CAS  Article  Google Scholar 

  6. 6

    Morris, J. J., Lenski, R. E. & Zinser, E. R. The black queen hypothesis: evolution of dependencies through adaptive gene loss. mBio 3, e00036–12 (2012).

    Article  Google Scholar 

  7. 7

    Giovannoni, S. J. et al. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309, 1242–1245 (2005).

    CAS  Article  Google Scholar 

  8. 8

    O'Malley, M. A., Wideman, J. G. & Ruiz-Trillo, I. Losing complexity: the role of simplification in macroevolution. Trends Ecol. Evol. 31, 608–621 (2016).

    Article  Google Scholar 

  9. 9

    Wernegreen, J. J. Endosymbiont evolution: predictions from theory and surprises from genomes. Ann. NY Acad. Sci. 1360, 16–35 (2015).

    CAS  Article  Google Scholar 

  10. 10

    Button, D. K. Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the Michaelis constant. Appl. Environ. Microbiol. 57, 2033–2038 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Biller, S. J., Berube, P. M., Lindell, D. & Chisholm, S. W. Prochlorococcus: the structure and function of collective diversity. Nat. Rev. Microbiol. 13, 13–27 (2015).

    CAS  Article  Google Scholar 

  12. 12

    Karcagi, I. et al. Indispensability of horizontally transferred genes and its impact on bacterial genome streamlining. Mol. Biol. Evol. 33, 1257–1269 (2016).

    CAS  Article  Google Scholar 

  13. 13

    Kurokawa, M., Seno, S., Matsuda, H. & Ying, B.-W. Correlation between genome reduction and bacterial growth. DNA Res. 23, 517–525 (2016).

    CAS  Article  Google Scholar 

  14. 14

    Kashtan, N. et al. Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344, 416–420 (2014).

    CAS  Article  Google Scholar 

  15. 15

    Luo, H., Swan, B. K., Stepanauskas, R., Hughes, A. L. & Moran, M. A. Comparing effective population sizes of dominant marine Alphaproteobacteria lineages. Environ. Microbiol. Rep. 6, 167–172 (2014).

    Article  Google Scholar 

  16. 16

    Charlesworth, B. Effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. 10, 195–205 (2009).

    CAS  Article  Google Scholar 

  17. 17

    Osburne, M. S., Holmbeck, B. M., Coe, A. & Chisholm, S. W. The spontaneous mutation frequencies of Prochlorococcus strains are commensurate with those of other bacteria. Environ. Microbiol. Rep. 3, 744–749 (2011).

    CAS  Article  Google Scholar 

  18. 18

    Sánchez-Baracaldo, P., Ridgwell, A. & Raven John, A. A neoproterozoic transition in the marine nitrogen cycle. Curr. Biol. 24, 652–657 (2014).

    Article  Google Scholar 

  19. 19

    Rocap, G. et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042–1047 (2003).

    CAS  Article  Google Scholar 

  20. 20

    Partensky, F. & Garczarek, L. Prochlorococcus: advantages and limits of minimalism. Ann. Rev. Mar. Sci. 2, 305–331 (2010).

    Article  Google Scholar 

  21. 21

    Luo, H., Friedman, R., Tang, J. & Hughes, A. L. Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus. Mol. Biol. Evol. 28, 2751–2760 (2011).

    CAS  Article  Google Scholar 

  22. 22

    Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015).

    Article  Google Scholar 

  23. 23

    Luo, H. Evolutionary origin of a streamlined marine bacterioplankton lineage. ISME J. 9, 1423–1433 (2015).

    Article  Google Scholar 

  24. 24

    Dayhoff, M., Eck, R. & Park, C. in Atlas of Protein Sequence and Structure (ed. Dayhoff, M. O. ) 89–100 (National Biomedical Research Foundation, 1972).

    Google Scholar 

  25. 25

    Zuckerkandl, E. & Pauling, L. in Evolving Genes and Proteins (eds Bryson, V. & Vogel, H. J. ) 97–116 (Academic, 1965).

    Google Scholar 

  26. 26

    Wernegreen, J. J. Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. PLoS ONE 6, e28905 (2011).

    CAS  Article  Google Scholar 

  27. 27

    Hughes, A. L. & Friedman, R. More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene 440, 50–56 (2009).

    CAS  Article  Google Scholar 

  28. 28

    Eyre-Walker, A., Keightley, P. D., Smith, N. G. C. & Gaffney, D. Quantifying the slightly deleterious mutation model of molecular evolution. Mol. Biol. Evol. 19, 2142–2149 (2002).

    CAS  Article  Google Scholar 

  29. 29

    Zhang, J. Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J. Mol. Evol. 50, 56–68 (2000).

    CAS  Article  Google Scholar 

  30. 30

    Hughes, A. L., Ota, T. & Nei, M. Positive Darwinian selection promotes charge profile diversity in the antigen-binding cleft of class I major-histocompatibility-complex molecules. Mol. Biol. Evol. 7, 515–524 (1990).

    CAS  PubMed  Google Scholar 

  31. 31

    Luo, H., Swan, B. K., Stepanauskas, R., Hughes, A. L. & Moran, M. A. Evolutionary analysis of a streamlined lineage of surface ocean roseobacters. ISME J. 8, 1428–1439 (2014).

    CAS  Article  Google Scholar 

  32. 32

    Moore, C. M. et al. Processes and patterns of oceanic nutrient limitation. Nat. Geosci. 6, 701–710 (2013).

    CAS  Article  Google Scholar 

  33. 33

    Grzymski, J. J. & Dussaq, A. M. The significance of nitrogen cost minimization in proteomes of marine microorganisms. ISME J. 6, 71–80 (2012).

    CAS  Article  Google Scholar 

  34. 34

    Biller, S. J. et al. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. Sci. Data 1, 140034 (2014).

    CAS  Article  Google Scholar 

  35. 35

    Nei, M. Molecular Evolutionary Genetics (Columbia Univ. Press, 1987).

    Google Scholar 

  36. 36

    Hughes, A. L. et al. Widespread purifying selection at polymorphic sites in human protein-coding loci. Proc. Natl Acad. Sci. USA 100, 15754–15757 (2003).

    CAS  Article  Google Scholar 

  37. 37

    Marais, G., Calteau, A. & Tenaillon, O. Mutation rate and genome reduction in endosymbiotic and free-living bacteria. Genetica 134, 205–210 (2008).

    Article  Google Scholar 

  38. 38

    Taddei, F. et al. Role of mutator alleles in adaptive evolution. Nature 387, 700–702 (1997).

    CAS  Article  Google Scholar 

  39. 39

    Sniegowski, P. D., Gerrish, P. J. & Lenski, R. E. Evolution of high mutation rates in experimental populations of E. coli. Nature 387, 703–705 (1997).

    CAS  Article  Google Scholar 

  40. 40

    Tenaillon, O., Toupance, B., Le Nagard, H., Taddei, F. & Godelle, B. Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria. Genetics 152, 485–493 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41

    Paul, S., Dutta, A., Bag, S., Das, S. & Dutta, C. Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus. BMC Genomics 11, 103 (2010).

    Article  Google Scholar 

  42. 42

    Viklund, J., Martijn, J., Ettema, T. J. G. & Andersson, S. G. E. Comparative and phylogenomic evidence that the Alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade. PLoS ONE 8, e78858 (2013).

    CAS  Article  Google Scholar 

  43. 43

    Amrine, K. C. H., Swingley, W. D. & Ardell, D. H. tRNA signatures reveal a polyphyletic origin of SAR11 strains among Alphaproteobacteria. PLoS Comput. Biol. 10, e1003454 (2014).

    Article  Google Scholar 

  44. 44

    Rodríguez-Ezpeleta, N. & Embley, T. M. The SAR11 group of Alpha-Proteobacteria is not related to the origin of mitochondria. PLoS ONE 7, e30520 (2012).

    Article  Google Scholar 

  45. 45

    Zaremba-Niedzwiedzka, K. et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome Biol. 14, R130 (2013).

    Article  Google Scholar 

  46. 46

    Thrash, J. C. et al. Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype. ISME J. 8, 1440–1451 (2014).

    Article  Google Scholar 

  47. 47

    Lee, H., Popodi, E., Tang, H. & Foster, P. L. Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing. Proc. Natl Acad. Sci. USA 109, E2774–E2783 (2012).

    CAS  Article  Google Scholar 

  48. 48

    Long, H. et al. Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans. Mol. Biol. Evol. 32, 2383–2392 (2015).

    CAS  Article  Google Scholar 

  49. 49

    Sung, W. et al. Asymmetric context-dependent mutation patterns revealed through mutation-accumulation experiments. Mol. Biol. Evol. 32, 1672–1683 (2015).

    CAS  Article  Google Scholar 

  50. 50

    Johnson, Z. I. et al. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311, 1737–1740 (2006).

    CAS  Article  Google Scholar 

  51. 51

    Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics 13, 555–556 (1997).

    CAS  Article  Google Scholar 

  52. 52

    Smith, N. C. Are radical and conservative substitution rates useful statistics in molecular evolution? J. Mol. Evol. 57, 467–478 (2003).

    CAS  Article  Google Scholar 

  53. 53

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    CAS  Article  Google Scholar 

Download references


This research was funded by the National Natural Science Foundation of China (41576141), the Hong Kong RGC Early Career Scheme (24101015), the Hong Kong Environment and Conservation Fund (15/2016), the Chinese University of Hong Kong (Direct Grants 4930062 and 4053105) and the US National Science Foundation (IIS 1161586 to J.T. and OCE-1232982 and DEB-1441717 to R.S.).

Author information




H.L. conceived and designed the study. Y.H. performed the research. R.S. and J.T. contributed reagent and analytic tools. H.L., Y.H., R.S. and J.T. analysed the data. H.L. wrote the paper.

Corresponding author

Correspondence to Haiwei Luo.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary Figures, Supplementary Table and Supplementary References. (PDF 8419 kb)

Supplementary Data

(1) Summary of simulation parameters used to estimate the dR/dC ratio based on charge classification of the 20 amino acids. (2) Summary of simulation parameters used to estimate the dR/dC ratio based on volume and polarity classification of the 20 amino acids. (XLSX 290 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Luo, H., Huang, Y., Stepanauskas, R. et al. Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes. Nat Microbiol 2, 17091 (2017). https://doi.org/10.1038/nmicrobiol.2017.91

Download citation

Further reading


Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing