Coherence of Microcystis species revealed through population genomics

Abstract

Microcystis is a genus of freshwater cyanobacteria, which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. Yet colony morphology is a plastic trait, which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes mainly from Canada and Brazil. We identified 17 Microcystis clusters of genomic similarity, five of which correspond to monophyletic clades containing at least three newly sequenced genomes. Four out of these five clades match to named morphospecies. Notably, M. aeruginosa is paraphyletic, distributed across 12 genomic clusters, suggesting it is not a coherent species. A few clades of closely related isolates are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clades further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes—including some involved in microcystin and micropeptin biosynthesis—are recombined between monophyletic groups in the same geographic location, suggesting local adaptation.

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Data availability

The raw reads and the Microcystis genomes contigs are available in GenBank under Bioproject number PRJNA507251 (Table S1).

References

  1. 1.

    Shapiro BJ. What microbial population genomics has taught us about speciation. In: Polz M, Rajora O (editors) Population genomics: Microorganisms Population genomics. Cham: Springer; 2018;31–47.

  2. 2.

    Wiedenbeck J, Cohan FM. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol Rev. 2011;35:957–76.

  3. 3.

    Whitaker RJ, Grogan DW, Taylor JW. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol Biol Evol. 2005;22:2354–61.

  4. 4.

    Cadillo-Quiroz H, Didelot X, Held NL, Herrera A, Darling A, Reno ML, et al. Patterns of gene flow define species of thermophilic Archaea. PLoS Biol. 2012;10:e1001265.

  5. 5.

    Bobay LM, Ochman H. Biological species are universal across Life’s domains. Genome Biol Evol. 2017;9:491–501.

  6. 6.

    Reno ML, Held NL, Fields CJ, Burke PV, Whitaker RJ. Biogeography of the Sulfolobus islandicus pan-genome. Proc Natl Acad Sci USA. 2009;106:8605–10.

  7. 7.

    Boucher Y, Cordero OX, Takemura A, Hunt DE, Schliep K, Bapteste E, et al. Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. MBio. 2011;2:e00335–10.

  8. 8.

    van Elsas JD, Bailey MJ. The ecology of transfer of mobile genetic elements. FEMS Microbiol Ecol. 2002;42:187–97.

  9. 9.

    Whittaker KA, Rynearson TA. Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow. Proc Natl Acad Sci USA. 2017;114:2651–6.

  10. 10.

    Humbert JF, Barbe V, Latifi A, Gugger M, Calteau A, Coursin T, et al. A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa. PLoS ONE. 2013;8:e70747.

  11. 11.

    Tanabe Y, Kaya K, Watanabe MM. Evidence for recombination in the microcystin synthetase (mcy) genes of toxic cyanobacteria Microcystis spp. J Mol Evol. 2004;58:633–41.

  12. 12.

    Tanabe Y, Kasai F, Watanabe MM. Multilocus sequence typing (MLST) reveals high genetic diversity and clonal population structure of the toxic cyanobacterium Microcystis aeruginosa. Microbiology. 2007;153:3695–703.

  13. 13.

    Tanabe Y, Sano T, Kasai F, Watanabe MM. Recombination, cryptic clades and neutral molecular divergence of the microcystin synthetase (mcy) genes of toxic cyanobacterium Microcystis aeruginosa. BMC Evol Biol. 2009;9:115.

  14. 14.

    van Gremberghe I, Leliaert F, Mergeay J, Vanormelingen P, Van der Gucht K, Debeer AE, et al. Lack of phylogeographic structure in the freshwater cyanobacterium Microcystis aeruginosa suggests global dispersal. PLoS ONE. 2011;6:e19561.

  15. 15.

    Harke MJ, Steffen MM, Gobler CJ, Otten TG, Wilhelm SW, Wood SA, et al. A review of the global ecology, genomics, and biogeography of the toxic cyanobacterium, Microcystis spp. Harmful Algae. 2016;54:4–20.

  16. 16.

    Shapiro BJ, Leducq JB, Mallet J. What is speciation? PLoS Genet. 2016;12:e1005860.

  17. 17.

    Otsuka S, Suda S, Li RH, Watanabe M, Oyaizu H, Matsumoto S, et al. Phylogenetic relationships between toxic and non-toxic strains of the genus Microcystis based on 16S to 23S internal transcribed spacer sequence. FEMS Microbiol Lett. 1999;172:15–21.

  18. 18.

    Otsuka S, Suda S, Shibata S, Oyaizu H, Matsumoto S, Watanabe MM. A proposal for the unification of five species of the cyanobacterial genus Microcystis Kutzing ex Lemmermann 1907 under the rules of the Bacteriological Code. Int J Syst Evol Microbiol. 2001;51:873–9.

  19. 19.

    Komárek J. Recent changes (2008) in cyanobacteria taxonomy based on a combination of molecular background with phenotype and ecological consequences (genus and species concept). Hydrobiologia. 2010;639:245–59.

  20. 20.

    Xiao M, Li M, Reynolds CS. Colony formation in the cyanobacterium Microcystis. Biol Rev Camb Philos Soc. 2018;93:1399–420.

  21. 21.

    Orr PT, Jones GJ. Relationship between microcystin production and cell division rates in nitrogen‐limited Microcystis aeruginosa cultures. Limnol Ocean. 1998;43:1604–14.

  22. 22.

    Compère P. The nomenclature of Cyanophyta under the Botanical Code. Arch Hydrobiol Suppl Algol Stud. 2005;117:31–7.

  23. 23.

    Zhang JY, Guan R, Zhang HJ, Li H, Xiao P, Yu GL, et al. Complete genome sequence and genomic characterization of Microcystis panniformis FACHB 1757 by third-generation sequencing. Stand Genom Sci. 2016;11:11.

  24. 24.

    Otsuka S, Suda S, Li RH, Matsumoto S, Watanabe MM. Morphological variability of colonies of Microcystis morphospecies in culture. J Gen Appl Microbiol. 2000;46:39–50.

  25. 25.

    Ma J, Brookes JD, Qin B, Paerl HW, Gao G, Wu P, et al. Environmental factors controlling colony formation in blooms of the cyanobacteria Microcystis spp. in Lake Taihu, China. Harmful Algae. 2014;31:136–42.

  26. 26.

    Wang WJ, Zhang YL, Shen H, Xie P, Yu J. Changes in the bacterial community and extracellular compounds associated with the disaggregation of Microcystis colonies. Biochem Syst Ecol. 2015;61:62–6.

  27. 27.

    Komárek J. A review of water-bloom forming Microcystis species, with regard to populations from Japan. Arch Hydrobiol Suppl Algol Stud. 1991;64:115–27.

  28. 28.

    Castenholz RW, Norris TB. Revisionary concepts of species in the cyanobacteria and their applications. Arch Hydrobiol Suppl Algol Stud. 2005;117:53–69.

  29. 29.

    Xu S, Sun Q, Zhou X, Tan X, Xiao M, Zhu W, et al. Polysaccharide biosynthesis-related genes explain phenotype-genotype correlation of Microcystis colonies in Meiliang Bay of Lake Taihu, China. Sci Rep. 2016;6:35551.

  30. 30.

    Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol. 2005;187:6258–64.

  31. 31.

    Christiansen G, Molitor C, Philmus B, Kurmayer R. Nontoxic strains of cyanobacteria are the result of major gene deletion events induced by a transposable element. Mol Biol Evol. 2008;25:1695–704.

  32. 32.

    Komárek J, Komárková-Legnerová J, Santanna CL, Azevedo MTP, Senna PC. Two common Microcystis species (Chroococcales, Cyanobacteria) from tropical America, including M. panniformis sp. nov. Cryptogam Algol. 2002;23:159–77.

  33. 33.

    Komárek J, Komárková J. Review of the European Microcystis-morphospecies (Cyanoprokaryotes) from nature. Czech Phycol. 2002;2:1–24.

  34. 34.

    Peng Y, Leung HC, Yiu SM, Chin FY. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 2012;28:1420–8.

  35. 35.

    Meyer KA, Davis TW, Watson SB, Denef VJ, Berry MA, Dick GJ. Genome sequences of lower Great Lakes Microcystis sp reveal strain-specific genes that are present and expressed in western Lake Erie blooms. PLoS ONE. 2017;12:e0183859.

  36. 36.

    Li Q, Lin F, Yang C, Wang J, Lin Y, Shen M, et al. A large-scale comparative metagenomic study reveals the functional interactions in six bloom-forming Microcystis-epibiont communities. Front Microbiol. 2018;9:746.

  37. 37.

    Eren AM, Esen OC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.

  38. 38.

    Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–U54.

  39. 39.

    Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 2016;26:1721–9.

  40. 40.

    Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinforma. 2010;11:119.

  41. 41.

    Hyatt D, LoCascio PF, Hauser LJ, Uberbacher EC. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics. 2012;28:2223–30.

  42. 42.

    Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.

  43. 43.

    Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma. 2004;5:113.

  44. 44.

    Stamatakis A, Aberer AJ, Goll C, Smith SA, Berger SA, Izquierdo-Carrasco F. RAxML-Light: a tool for computing terabyte phylogenies. Bioinformatics. 2012;28:2064–6.

  45. 45.

    Angiuoli SV, Salzberg SL. Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics. 2011;27:334–42.

  46. 46.

    Cheng L, Connor TR, Siren J, Aanensen DM, Corander J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol. 2013;30:1224–8.

  47. 47.

    Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA. 2009;106:19126–31.

  48. 48.

    Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA. 2005;102:2567–72.

  49. 49.

    Konstantinidis KT, Ramette A, Tiedje JM. Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl Environ Microbiol. 2006;72:7286–93.

  50. 50.

    Wickham H. Elegant graphics for data analysis. New York: Springer-Verlag; 2016.

  51. 51.

    Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31:3691–3.

  52. 52.

    Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol. 2015;11:e1004041.

  53. 53.

    Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.

  54. 54.

    Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.

  55. 55.

    Price MN, Dehal PS, Arkin AP. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.

  56. 56.

    Asnicar F, Weingart G, Tickle TL, Huttenhower C, Segata N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ. 2015;3:e1029.

  57. 57.

    Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucl Acids Res. 2016;44:D286–93.

  58. 58.

    Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol. 2017;34:2115–22.

  59. 59.

    Blin K, Wolf T, Chevrette MG, Lu X, Schwalen CJ, Kautsar SA, et al. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification. Nucl Acids Res. 2017;45:W36–41.

  60. 60.

    Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res. 1997;25:3389–402.

  61. 61.

    Castillo-Ramirez S, Corander J, Marttinen P, Aldeljawi M, Hanage WP, Westh H, et al. Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus. Genome Biol. 2012;13:R126.

  62. 62.

    Belykh OI, Dmitrieva OA, Gladkikh AS, Sorokovikova EG. Identification of toxigenic Cyanobacteria of the genus Microcystis in the Curonian Lagoon (Baltic Sea). Oceanology+. 2013;53:71–9.

  63. 63.

    Makarova KS, Grishin NV, Koonin EV. The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria. Bioinformatics. 2006;22:2581–4.

  64. 64.

    Makarova KS, Wolf YI, Koonin EV. Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct. 2009;4:19.

  65. 65.

    Makarova KS, Wolf YI, Snir S, Koonin EV. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol. 2011;193:6039–56.

  66. 66.

    Welker M, von Dohren H. Cyanobacterial peptides—nature’s own combinatorial biosynthesis. FEMS Microbiol Rev. 2006;30:530–63.

  67. 67.

    Sussmuth RD, Mainz A. Nonribosomal peptide synthesis-principles and prospects. Angew Chem Int Ed Engl. 2017;56:3770–821.

  68. 68.

    Tillett D, Parker DL, Neilan BA. Detection of toxigenicity by a probe for the microcystin synthetase A gene (mcyA) of the cyanobacterial genus Microcystis: comparison of toxicities with 16S rRNA and phycocyanin operon (Phycocyanin Intergenic Spacer) phylogenies. Appl Environ Microbiol. 2001;67:2810–8.

  69. 69.

    Pearson LA, Dittmann E, Mazmouz R, Ongley SE, D’Agostino PM, Neilan BA. The genetics, biosynthesis and regulation of toxic specialized metabolites of cyanobacteria. Harmful Algae. 2016;54:98–111.

  70. 70.

    Via-Ordorika L, Fastner J, Kurmayer R, Hisbergues M, Dittmann E, Komarek J, et al. Distribution of microcystin-producing and non-microcystin-producing Microcystis sp. in European freshwater bodies: detection of microcystins and microcystin genes in individual colonies. Syst Appl Microbiol. 2004;27:592–602.

  71. 71.

    Yoshida M, Yoshida T, Satomi M, Takashima Y, Hosoda N, Hiroishi S. Intra-specific phenotypic and genotypic variation in toxic cyanobacterial Microcystis strains. J Appl Microbiol. 2008;105:407–15.

  72. 72.

    Xu Y, Wu Z, Yu B, Peng X, Yu G, Wei Z, et al. Non-microcystin producing Microcystis wesenbergii (Komarek) Komarek (Cyanobacteria) representing a main waterbloom-forming species in Chinese waters. Environ Pollut. 2008;156:162–7.

  73. 73.

    Otten TG, Paerl HW. Phylogenetic inference of colony isolates comprising seasonal Microcystis blooms in Lake Taihu, China. Micro Ecol. 2011;62:907–18.

  74. 74.

    Majewski J, Cohan FM. Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics. 1999;152:1459–74.

  75. 75.

    Jain C, Rodriguez RL, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:5114.

  76. 76.

    Moreira C, Spillane C, Fathalli A, Vasconcelos V, Antunes A. African origin and europe-mediated global dispersal of the cyanobacterium Microcystis aeruginosa. Curr Microbiol. 2014;69:628–33.

  77. 77.

    Marmen S, Aharonovich D, Grossowicz M, Blank L, Yacobi YZ, Sher DJ. Distribution and habitat specificity of potentially-toxic Microcystis across climate, land, and water use gradients. Front Microbiol. 2016;7:271.

  78. 78.

    Fraser C, Hanage WP, Spratt BG. Recombination and the nature of bacterial speciation. Science. 2007;315:476–80.

  79. 79.

    Vos M, Didelot X. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 2009;3:199–208.

  80. 80.

    Shapiro BJ, Polz MF. Ordering microbial diversity into ecologically and genetically cohesive units. Trends Microbiol. 2014;22:235–47.

  81. 81.

    Imai H, Chang KH, Kusaba M, Nakano S. Temperature-dependent dominance of Microcystis (Cyanophyceae) species: M. aeruginosa and M. wesenbergii. J Plankton Res. 2009;31:171–8.

  82. 82.

    Rantala A, Fewer DP, Hisbergues M, Rouhiainen L, Vaitomaa J, Borner T, et al. Phylogenetic evidence for the early evolution of microcystin synthesis. Proc Natl Acad Sci USA. 2004;101:568–73.

  83. 83.

    Mikalsen B, Boison G, Skulberg OM, Fastner J, Davies W, Gabrielsen TM, et al. Natural variation in the microcystin synthetase operon mcyABC and impact on microcystin production in Microcystis strains. J Bacteriol. 2003;185:2774–85.

  84. 84.

    Tooming-Klunderud A, Fewer DP, Rohrlack T, Jokela J, Rouhiainen L, Sivonen K, et al. Evidence for positive selection acting on microcystin synthetase adenylation domains in three cyanobacterial genera. BMC Evol Biol. 2008;8:256.

  85. 85.

    Moreira C, Vasconcelos V, Antunes A. Phylogeny of microcystins: evidence of a biogeographical trend? Curr Microbiol. 2013;66:214–21.

  86. 86.

    Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, et al. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol. 2015;13:722–36.

  87. 87.

    Godde JS, Bickerton A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol. 2006;62:718–29.

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Acknowledgements

We are grateful to David Bird, Naíla Barbosa da Costa, Mylène Boyer, Julie Marleau, and Coralie Deladrière for assistance isolating strains and maintaining cultures. This work was supported by the Genome Québec and Genome Canada-funded ATRAPP Project (Algal blooms, Treatment, Risk Assessment, Prediction, and Prevention). NT was funded by a project from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 656647. Cultures collections (Brazilian and some Canadian strains) were partially obtained and maintained thanks to CNPq and FAPEMIG grants to AG. We also want to acknowledge the financial support of the National Research Council.

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Correspondence to Olga M. Pérez-Carrascal or Nicolas Tromas.

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Pérez-Carrascal, O.M., Terrat, Y., Giani, A. et al. Coherence of Microcystis species revealed through population genomics. ISME J 13, 2887–2900 (2019) doi:10.1038/s41396-019-0481-1

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