Ordering microbial diversity into ecologically and genetically cohesive units

Trends in Microbiology

Volumn 22, Issue 5, 2014, Pages 235-247

  Shapiro, B Jesse ^a   Polz, Martin F ^b  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Ecological differentiation; Gene flow; Mosaic sympatric speciation; Population genomics; Reverse ecology; Selective sweeps

Indexed keywords

RNA 16S;

CYANOBACTERIUM; GENE FLOW; GENE MUTATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HOMOLOGOUS RECOMBINATION; HORIZONTAL GENE TRANSFER; METAGENOME; MICROBIAL DIVERSITY; MICROBIAL POPULATION DYNAMICS; MICROHABITAT; NITROGEN FIXATION; NONHUMAN; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; PROCHLOROCOCCUS; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SULFOLOBUS; BIOTA; GENETIC RECOMBINATION; GENETIC SELECTION; MUTATION; PHYLOGEOGRAPHY;

BIOTA; GENE TRANSFER, HORIZONTAL; GENETIC VARIATION; MUTATION; PHYLOGEOGRAPHY; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84899979623     PISSN: 0966842X     EISSN: 18784380     Source Type: Journal    
DOI: 10.1016/j.tim.2014.02.006     Document Type: Review

References (85)

1. Gevers D., et al. Opinion: re-evaluating prokaryotic species. Nat. Rev. Microbiol. 2005, 3:733-739.
2. Cohan F.M., Koeppel A.F. The origins of ecological diversity in prokaryotes. Curr. Biol. 2008, 18:1024-1034.
3. Mayr E. Systematics and the Origin of Species 1942, Columbia University Press.
4. Syvanen M. Evolutionary implications of horizontal gene transfer. Annu. Rev. Genet. 2012, 46:341-358.
5. Danchin E.G.J., Rosso M-N. Lateral gene transfers have polished animal genomes: lessons from nematodes. Front. Cell. Infect. Microbiol. 2012, 2:27.
6. Schönknecht G., et al. Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Bioessays 2013, 36:9-20.
7. Mallet J. Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philos. Trans. R. Soc. Lond. B 2008, 363:2971-2986.
8. de Vries J., Wackernagel W. Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:2094-2099.
9. Mell J.C., et al. Transformation of natural genetic variation into Haemophilus influenzae genomes. PLoS Pathog. 2011, 7:e1002151.
10. Cordero O.X., et al. Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:20059-20064.
11. Croucher N.J., et al. A high-resolution view of genome-wide pneumococcal transformation. PLoS Pathog. 2012, 8:e1002745.
12. Doolittle W.F., Papke R.T. Genomics and the bacterial species problem. Genome Biol. 2006, 7:116.
13. Hahn M.W., Pockl M. Ecotypes of planktonic Actinobacteria with identical 16S rRNA genes adapted to thermal niches in temperate, subtropical, and tropical freshwater habitats. Appl. Environ. Microbiol. 2005, 71:766-773.
14. Doolittle W.F., Zhaxybayeva O. On the origin of prokaryotic species. Genome Res. 2009, 19:744-756.
15. Wiedenbeck J., Cohan F.M. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol. Rev. 2011, 35:957-976.
16. Hanage W.P., et al. Fuzzy species among recombinogenic bacteria. BMC Biol. 2005, 3:6.
17. Luo C., et al. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:7200-7205.
18. Konstantinidis K.T., Delong E.F. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J. 2008, 2:1052-1065.
19. Oh S., et al. Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl. Environ. Microbiol. 2011, 77:6000-6011.
20. Denef V.J., et al. AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J. 2010, 4:599-610.
21. Simmons S.L., et al. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol. 2008, 6:1427-1442.
22. Whitaker R.J., et al. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 2003, 301:976-978.
23. Reno M.L., et al. Biogeography of the Sulfolobus islandicus pan-genome. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:8605-8610.
24. Welch R.A., et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:17020-17024.
25. Kettler G.C., et al. Patterns and implications of gene gain and loss in the evolution of Prochlorococcus. PLoS Genet. 2007, 3:2515-2528.
26. Cordero O.X., Polz M.F. Explaining microbial genomic diversity in light of evolutionary ecology. Nat. Rev. Microbiol. 2014, 10.1038/nrmicro3218.
27. Coleman M.L., Chisholm S.W. Ecosystem-specific selection pressures revealed through comparative population genomics. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:18634-18639.
28. Polz M.F., et al. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos. Trans. R. Soc. Lond. B 2006, 361:2009-2021.
29. Jax K. Ecological units: definitions and application. Q. Rev. Biol. 2006, 81:237-258.
30. Li Y.F., et al. 'Reverse ecology' and the power of population genomics. Evolution 2008, 62:2984-2994.
31. Levy R., Borenstein E. Reverse ecology: from systems to environments and back. Adv. Exp. Med. Biol. 2012, 751:329-345.
32. Ellison C.E., et al. Population genomics and local adaptation in wild isolates of a model microbial eukaryote. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:2831-2836.
33. Konstantinidis K.T., Tiedje J.M. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 2005, 187:6258-6264.
34. Hanson C.A., et al. Beyond biogeographic patterns: processes shaping the microbial landscape. Nat. Rev. Microbiol. 2012, 10:497-506.
35. Nemergut D.R., et al. Global patterns in the biogeography of bacterial taxa. Environ. Microbiol. 2010, 13:135-144.
36. Vos M. A species concept for bacteria based on adaptive divergence. Trends Microbiol. 2011, 19:1-7.
37. Smith J.M., et al. How clonal are bacteria?. Proc. Natl. Acad. Sci. U.S.A. 1993, 90:4384-4388.
38. Vos M., Didelot X. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 2009, 3:199-208.
39. Vulić M., et al. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl. Acad. Sci. U.S.A. 1997, 94:9763-9767.
40. Majewski J.J., Cohan F.M.F. DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 1999, 153:1525-1533.
41. Grogan D.W., Stengel K.R. Recombination of synthetic oligonucleotides with prokaryotic chromosomes: substrate requirements of the Escherichia coli/λRed and Sulfolobus acidocaldarius recombination systems. Mol. Microbiol. 2008, 69:1255-1265.
42. Naor A., et al. Low species barriers in halophilic archaea and the formation of recombinant hybrids. Curr. Biol. 2012, 22:1444-1448.
43. Whitaker R.J., et al. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol. Biol. Evol. 2005, 22:2354-2361.
44. Williams D., et al. Quantifying homologous replacement of loci between haloarchaeal species. Genome Biol. Evol. 2012, 4:1223-1244.
45. Fraser C., et al. Recombination and the nature of bacterial speciation. Science 2007, 315:476-480.
46. Barrick J.E., et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 2009, 461:1243-1247.
47. Blount Z.D., et al. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 2012, 488:513-518.
48. Shapiro B.J., et al. Looking for Darwin's footprints in the microbial world. Trends Microbiol. 2009, 17:196-204.
49. Friedman J., et al. Sympatric speciation: when is it possible in bacteria?. PLoS ONE 2013, 8:e53539.
50. Cornejo O.E., et al. Polymorphic competence peptides do not restrict recombination in Streptococcus pneumoniae. Mol. Biol. Evol. 2010, 27:694-702.
51. Polz M.F., et al. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet. 2013, 29:170-175.
52. Hunt D.E., et al. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 2008, 320:1081-1085.
53. Koeppel A., et al. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:2504-2509.
54. Rocap G., et al. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 2003, 424:1042-1047.
55. Johnson Z.I., et al. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 2006, 311:1737-1740.
56. Yawata Y., et al. A competition-dispersal trade-off ecologically differentiates recently speciated marine bacterioplankton populations. Proc. Natl. Acad. Sci. U.S.A. 2014, (in press).
57. Shapiro B.J., et al. Population genomics of early events in the ecological differentiation of bacteria. Science 2012, 336:48-51.
58. Cadillo-Quiroz H., et al. Patterns of gene flow define species of thermophilic archaea. PloS Biol. 2012, 10:e1001265.
59. Via S. Divergence hitchhiking and the spread of genomic isolation during ecological speciation-with-gene-flow. Philos. Trans. R. Soc. Lond. B 2012, 367:451-460.
60. Papke R.T., et al. Searching for species in haloarchaea. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:14092-14097.
61. Denef V.J., et al. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:2383-2390.
62. Burke C., et al. Bacterial community assembly based on functional genes rather than species. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:14288-14293.
63. Boucher Y., et al. Local mobile gene pools rapidly cross species boundaries to create endemicity within global Vibrio cholerae populations. mBio 2011, 2:e00335-e410.
64. Katz L.S., et al. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti. mBio 2013, 4:e00398-e413.
65. Rodriguez-Valera F., et al. Explaining microbial population genomics through phage predation. Nat. Rev. Microbiol. 2009, 7:828-836.
66. Cordero O.X., et al. Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance. Science 2012, 337:1228-1231.
67. Lieberman T.D., et al. Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures. Nat. Genet. 2013, 46:82-87.
68. Szabó G., et al. Reproducibility of Vibrionaceae population structure in coastal bacterioplankton. ISME J. 2013, 7:509-519.
69. Shapiro B.J. Signatures of natural selection and ecological differentiation in microbial genomes. Adv. Exp. Med. Biol. 2014, 781:339-359.
70. Berg O.G., Kurland C.G. Evolution of microbial genomes: sequence acquisition and loss. Mol. Biol. Evol. 2002, 19:2265-2276.
71. Thompson J.R., et al. Genotypic diversity within a natural coastal bacterioplankton population. Science 2005, 307:1311-1313.
72. Haegeman B., Weitz J.S. A neutral theory of genome evolution and the frequency distribution of genes. BMC Genomics 2012, 13:196.
73. Castillo-Ramírez S., et al. The impact of recombination on dN/dS within recently emerged bacterial clones. PLoS Pathog. 2011, 7:e1002129.
74. Sheppard S.K., et al. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:11923-11927.
75. Falush D., Bowden R. Genome-wide association mapping in bacteria?. Trends Microbiol. 2006, 14:353-355.
76. Sokurenko E.V. Selection footprint in the FimH adhesin shows pathoadaptive niche differentiation in Escherichia coli. Mol. Biol. Evol. 2004, 21:1373-1383.
77. Chattopadhyay S., et al. Tracking recent adaptive evolution in microbial species using TimeZone. Nat. Protoc. 2013, 8:652-665.
78. Farhat M.R., et al. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat. Genet. 2013, 45:1183-1189.
79. Marttinen P., et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 2012, 40:e6.
80. Didelot X., et al. Inference of homologous recombination in bacteria using whole-genome sequences. Genetics 2010, 186:1435-1449.
81. Majewski J., Cohan F.M. Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics 1999, 152:1459-1474.
82. Caro-Quintero A., et al. Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species. J. Bacteriol. 2009, 191:5824-5831.
83. Caro-Quintero A., Konstantinidis K.T. Bacterial species may exist, metagenomics reveal. Environ. Microbiol. 2011, 14:347-355.
84. Cohan F.M. Bacterial species and speciation. Syst. Biol. 2001, 50:513-524.
85. Koeppel A.F., et al. Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species. ISME J. 2013, 7:1080-1091.