Antonie van Leeuwenhoek

, Volume 103, Issue 1, pp 99–119

Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov.

Original Paper

Abstract

The phylum “Chloroflexi” contains highly divergent groups of bacteria. To understand the evolutionary relationships among these bacteria, phylogenetic trees were constructed based upon concatenated sequences for 20 conserved proteins and comparative genomic analyses were carried out to identify molecular markers (conserved signature indels or CSIs) that are specific for different clades of Chloroflexi. In phylogenetic trees based upon either concatenated protein sequences or the 16S rRNA gene, species from the class Chloroflexi and the order Chloroflexales formed strongly supported clades. The species from these clades are also clearly distinguished from other bacteria based upon 5 and 9 identified CSIs, respectively, in important proteins that were specific for these clades. Additionally, three CSIs that were specific for the genus Chloroflexus and four CSIs specific for the genus Roseiflexus were also identified. In phylogenetic trees, the species Oscillochloris trichoides (family Oscillochloridaceae) formed a strongly supported clade with the species from the genus Chloroflexus (and with Chloronema in the 16S rRNA gene tree). A specific relationship of O. trichoides to the Chloroflexus spp. is also strongly supported by 7 CSIs that are uniquely shared by the species from these genera but not found in Roseiflexus or any other bacteria. In addition to their phylogenetic clustering and shared presence of many novel CSIs, the species from the genera Chloroflexus and Oscillochloris (and also Chloronema) also differ from species of the genera Roseiflexus (and Heliothrix) by their green color, shared presence of the chlorosomes and Bchl c (in addition to Bchl a and d in some species), by their fatty acid profiles, and by the presence of β- and γ-carotenes and quinone MK-10. Based upon these observations, we propose division of the order Chloroflexales into two suborders: the first of these suborders Chloroflexineae subord. nov. is comprised of the family Oscillochloridaceae (emended to include the genus Chloronema) and a new family Chloroflexaceae fam. nov. consisting of the genus Chloroflexus. The second suborder Roseiflexineae subord. nov. contains a new family Roseiflexaceae fam. nov. comprised of the genera Roseiflexus and Heliothrix; orange-red bacteria lacking chlorosomes and Bchl c and differing from the Chloroflexineae in their carotenoids, quinones and fatty acid profiles. Additionally, we also provide here formal descriptions of the class Chloroflexi class. nov., and of the orders Chloroflexales ord. nov. and Herpetosiphonales ord. nov. Lastly, our phylogenetic and comparative analyses provide either no or very weak support for a grouping together of the different classes (viz. Chloroflexi, Thermomicrobia, Dehalococcoidetes, Anaerolineae, Caldilineae and Ktedonobacteria) that are currently part of the phylum Chloroflexi. However, a specific grouping of the classes Chloroflexi and Thermomicrobia (as well as ‘Thermobaculum’) is supported by both phylogenetic means and the identified CSIs. Based upon these results, it is suggested that the phylum Chloroflexi “sensu stricto” should be comprised only of the classes Chloroflexi and Thermomicrobia and the other four classes (viz. Dehalococcoidetes, Anaerolineae, Caldilineae and Ktedonobacteria), which are at present part of this “superphylum” should be regarded as taxa related to the phylum Chloroflexi “sensu stricto”, awaiting more detailed investigations to clarify their relationships to each other and other phyla of bacteria.

Keywords

Chloroflexi Thermomicrobia Chloroflexi taxonomy Suborders Chloroflexineae and Roseiflexineae Chloroflexaceae family Oscillochloridaceae family Roseiflexaceae family Conserved signature indels Phylogenetic trees 

Supplementary material

10482_2012_9790_MOESM1_ESM.pdf (405 kb)
Supplementary material 1 (PDF 405 kb)

References

  1. Baldauf SL, Palmer JD (1993) Animals and fungi are each other’s closest relatives: congruent evidence from multiple proteins. Proc Natl Acad Sci USA 90:11558–11562PubMedCrossRefGoogle Scholar
  2. Bhandari V, Gupta RS (2012) Molecular signatures for the phylum Synergistetes and some of its subclades. Antonie van Leeuwenhoek. doi:10.1007/s10482-012-9759-2
  3. Blankenship RE (1992) Origin and early evolution of photosynthesis. Photosynth Res 33:91–111PubMedCrossRefGoogle Scholar
  4. Blankenship RE (2010) Early evolution of photosynthesis. Plant Physiol 154:434–438PubMedCrossRefGoogle Scholar
  5. Bryant DA, Frigaard NU (2006) Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol 14:488–496PubMedCrossRefGoogle Scholar
  6. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552PubMedCrossRefGoogle Scholar
  7. Castenholz RW (2001a) Class, “Chloroflexi”. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology. The Archaea and the deeply branching and phototrophic bacteria, 2nd edn, vol 1. Springer Verlag, New York, pp 427Google Scholar
  8. Castenholz RW (2001b) Order II. “Herpetosiphonales”. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology. The Archaea and the deeply branching and phototrophic bacteria, 2nd edn, vol 1. Springer Verlag, New York, pp 444–446Google Scholar
  9. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287PubMedCrossRefGoogle Scholar
  10. Cole JR, Wang Q, Cardenas E et al (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37:D141–D145PubMedCrossRefGoogle Scholar
  11. Collins AM, Xin Y, Blankenship RE (2009) Pigment organization in the photosynthetic apparatus of Roseiflexus castenholzii. Biochim Biophys Acta 1787:1050–1056PubMedCrossRefGoogle Scholar
  12. Euzeby JP (2011) List of prokaryotic names with standing in nomenclature. http://www.bacterio.cict.fr/classifphyla.html. Accessed 20 July 2012
  13. Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22(521–65):521–565PubMedCrossRefGoogle Scholar
  14. Gao B, Gupta RS (2012a) Microbial systematics in the post-genomics era. Antonie Van Leeuwenhoek 101:45–54PubMedCrossRefGoogle Scholar
  15. Gao B, Gupta RS (2012b) Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 76:66–112PubMedCrossRefGoogle Scholar
  16. Garrity GM, Holt JG (2001a) Phylum BVI, Chloroflexi phy. nov. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology : The Archaea and the deeply branching and phototrophic bacteria, vol 1. 2nd edn. Springer, New York, pp 427–446Google Scholar
  17. Garrity GM, Holt JG (2001b) Phylum BVIi. Thermomicrobia phy. nov. In: Boone DR, Castenholz RW (eds) Bergey’s manual of systematic bacteriology. The Archaea and the deeply branching and phototrophic Bacteria, vol 1. 2nd edn. Springer, New York, pp 447–450Google Scholar
  18. Garrity GM, Bell JA, Lilburn TG (2005) The revised road map to the manual. In: Brenner DJ, Krieg NR, Staley JT (eds) Berge1y’s manual of systematic bacteriology. Springer, New York, pp 159–220CrossRefGoogle Scholar
  19. Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62:1435–1491PubMedGoogle Scholar
  20. Gupta RS (2003) Evolutionary relationships among photosynthetic bacteria. Photosynth Res 76:173–183PubMedCrossRefGoogle Scholar
  21. Gupta RS (2009) Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Evol Microbiol 59:2510–2526PubMedCrossRefGoogle Scholar
  22. Gupta RS (2010a) Applications of conserved indels for understanding microbial phylogeny. In: Oren A, Papke RT (eds) Molecular phylogeny of microorganisms. Caister Academic Press, Norfolk, pp 135–150Google Scholar
  23. Gupta RS (2010b) Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups. Photosynth Res 104:357–372PubMedCrossRefGoogle Scholar
  24. Gupta RS (2011) Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes. Antonie Van Leeuwenhoek 100:171–182PubMedCrossRefGoogle Scholar
  25. Gupta RS (2012) Origin and spread of photosynthesis based upon conserved sequence features in key bacteriochlorophyll biosynthesis proteins. Mol Biol Evol. doi:10.1093/molbev/ss145
  26. Gupta RS, Bhandari V (2011) Phylogeny and molecular signatures for the phylum thermotogae and its subgroups. Antonie Van Leeuwenhoek 100:1–34PubMedCrossRefGoogle Scholar
  27. Gupta RS, Griffiths E (2002) Critical issues in bacterial phylogeny. Theor Popul Biol 61:423–434PubMedCrossRefGoogle Scholar
  28. Gupta RS, Johari V (1998) Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-Thermus group and Cyanobacteria. J Mol Evol 46:716–720PubMedCrossRefGoogle Scholar
  29. Gupta RS, Shami A (2011) Molecular signatures for the Crenarchaeota and the Thaumarchaeota. Antonie Van Leeuwenhoek 99:133–157PubMedCrossRefGoogle Scholar
  30. Gupta RS, Mukhtar T, Singh B (1999) Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. Mol Microbiol 32:893–906PubMedCrossRefGoogle Scholar
  31. Hanada S, Pierson BK (2006) The Family Chloroflexaceae. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria. Springer, New York, pp 815–842Google Scholar
  32. Hanada S, Hiraishi A, Shimada K, Matsuura K (1995) Chloroflexus aggregans sp. nov., a filamentous phototrophic bacterium which forms dense cell aggregates by active gliding movement. Int J Syst Bacteriol 45:676–681PubMedCrossRefGoogle Scholar
  33. Hanada S, Takaichi S, Matsuura K, Nakamura K (2002) Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. Int J Syst Evol Microbiol 52:187–193PubMedCrossRefGoogle Scholar
  34. Hohmann-Marriott MF, Blankenship RE (2007) Hypothesis on chlorosome biogenesis in green photosynthetic bacteria. FEBS Lett 581:800–803PubMedCrossRefGoogle Scholar
  35. Hugenholtz P, Stackebrandt E (2004) Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 54:2049–2051PubMedCrossRefGoogle Scholar
  36. Ivanovsky RN, Fal YI, Berg IA et al (1999) Evidence for the presence of the reductive pentose phosphate cycle in a filamentous anoxygenic photosynthetic bacterium, Oscillochloris trichoides strain DG-6. Microbiology 145(Pt 7):1743–1748PubMedCrossRefGoogle Scholar
  37. Keppen OI, Tourova TP, Kuznetsov BB, Ivanovsky RN, Gorlenko VM (2000) Proposal of Oscillochloridaceae fam. nov. on the basis of a phylogenetic analysis of the filamentous anoxygenic phototrophic bacteria, and emended description of Oscillochloris and Oscillochloris trichoides in comparison with further new isolates. Int J Syst Evol Microbiol 50(Pt 4):1529–1537PubMedCrossRefGoogle Scholar
  38. Kiss H, Cleland D, Lapidus A et al (2010) Complete genome sequence of ‘Thermobaculum terrenum’ type strain (YNP1). Stand Genomic Sci 3:153–162PubMedCrossRefGoogle Scholar
  39. Kiss H, Nett M, Domin N et al (2011) Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114–95T). Stand Genomic Sci 5:356–370PubMedCrossRefGoogle Scholar
  40. Kube M, Beck A, Zinder SH, Kuhl H, Reinhardt R, Adrian L (2005) Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol 23:1269–1273PubMedCrossRefGoogle Scholar
  41. Kunisawa T (2011) The phylogenetic placement of the non-phototrophic, Gram-positive thermophile ‘Thermobaculum terrenum’ and branching orders within the phylum ‘Chloroflexi’ inferred from gene order comparisons. Int J Syst Evol Microbiol 61:1944–1953PubMedCrossRefGoogle Scholar
  42. Kuznetsov BB, Ivanovsky RN, Keppen OI et al (2011) Draft genome sequence of the anoxygenic filamentous phototrophic bacterium Oscillochloris trichoides subsp. DG-6. J Bacteriol 193:321–322PubMedCrossRefGoogle Scholar
  43. Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948PubMedCrossRefGoogle Scholar
  44. Lu GN, Tao XQ, Huang W, Dang Z, Li Z, Liu CQ (2010) Dechlorination pathways of diverse chlorinated aromatic pollutants conducted by Dehalococcoides sp. strain CBDB1. Sci Total Environ 408:2549–2554PubMedCrossRefGoogle Scholar
  45. Ludwig W, Klenk H-P (2005) Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergey’s manual of systematic bacteriology. Springer, Berlin, pp 49–65CrossRefGoogle Scholar
  46. McMurdie PJ, Behrens SF, Muller JA et al (2009) Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet 5:e1000714PubMedCrossRefGoogle Scholar
  47. Moe WM, Yan J, Nobre MF, da Costa MS, Rainey FA (2009) Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater. Int J Syst Evol Microbiol 59:2692–2697PubMedCrossRefGoogle Scholar
  48. Mulkidjanian AY, Koonin EV, Makarova KS et al (2006) The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci USA 103:13126–13131PubMedCrossRefGoogle Scholar
  49. Naushad HS, Gupta RS (2012) Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades. Antonie Van Leeuwenhoek 101:105–124PubMedCrossRefGoogle Scholar
  50. Olson JM, Pierson BK (1987) Evolution of reaction centers in photosynthetic prokaryotes. Int Rev Cytol 108:209–248PubMedCrossRefGoogle Scholar
  51. Pati A, Labutti K, Pukall R et al (2010) Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022). Stand Genomic Sci 2:49–56PubMedCrossRefGoogle Scholar
  52. Pierson BK (1994) The emergence, diversification, and role of photosynthetic eubacteria. In: Benston S (ed) Early Life on Earth: Nobel Symposium No. 84, Columbia University Press, New York, pp 161–180Google Scholar
  53. Pierson BK (2001) Family 1. “Chloroflexaceae” filamentous anoxygenic phototrophic bacteria. In: Boone DR, Castenholz RW, Garrity GM (eds) Bergey’s manual of systematic bacteriology. The Archaea and the deeply branching and phototrophic bacteria, 2nd edn, vol 1. Springer Verlag, New York, pp 427–429Google Scholar
  54. Pierson BK, Castenholz RW (1974) A phototrophic gliding filamentous bacterium of hot springs, Chloroflexus aurantiacus, gen. and sp. nov. Arch Microbiol 100:5–24Google Scholar
  55. Pierson BK, Castenholz RW (1992) The Family Chloroflexaceae. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer KH (eds) The Prokaryotes. Springer, New York, pp 3754–3775Google Scholar
  56. Pierson BK, Giovannoni SJ, Stahl DA, Castenholz RW (1985) Heliothrix oregonensis, gen. nov., sp. nov., a phototrophic filamentous gliding bacterium containing bacteriochlorophyll a. Arch Microbiol 142:164–167PubMedCrossRefGoogle Scholar
  57. Psencik J, Collins AM, Liljeroos L et al (2009) Structure of chlorosomes from the green filamentous bacterium Chloroflexus aurantiacus. J Bacteriol 191:6701–6708PubMedCrossRefGoogle Scholar
  58. Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE (2002) Whole-genome analysis of photosynthetic prokaryotes. Science 298:1616–1620PubMedCrossRefGoogle Scholar
  59. Rivera MC, Lake JA (1992) Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257:74–76PubMedCrossRefGoogle Scholar
  60. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502–504PubMedCrossRefGoogle Scholar
  61. Seshadri R, Adrian L, Fouts DE et al (2005) Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307:105–108PubMedCrossRefGoogle Scholar
  62. Sutcliffe IC (2010) A phylum level perspective on bacterial cell envelope architecture. Trends Microbiol 18:464–470PubMedCrossRefGoogle Scholar
  63. Sutcliffe IC (2011) Cell envelope architecture in the Chloroflexi: a shifting frontline in a phylogenetic turf war. Environ Microbiol 13:279–282PubMedCrossRefGoogle Scholar
  64. Taisova AS, Keppen OI, Lukashev EP, Arutyunyan AM, Fetisova ZG (2002) Study of the chlorosomal antenna of the green mesophilic filamentous bacterium Oscillochloris trichoides. Photosynth Res 74:73–85PubMedCrossRefGoogle Scholar
  65. Takaichi S, Maoka T, Yamada M, Matsuura K, Haikawa Y, Hanada S (2001) Absence of carotenes and presence of a tertiary methoxy group in a carotenoid from a thermophilic filamentous photosynthetic bacterium Roseiflexus castenholzii. Plant Cell Physiol 42:1355–1362PubMedCrossRefGoogle Scholar
  66. Tang KH, Barry K, Chertkov O et al (2011a) Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus. BMC Genomics 12:334PubMedCrossRefGoogle Scholar
  67. Tang KH, Tang YJ, Blankenship RE (2011b) Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications. Front Microbiol 2:165PubMedGoogle Scholar
  68. Trüper HG (1976) Higher taxa of the phototrophic bacteria: Chloroflexaceae fam. nov., family for the gliding, filamentous phototrophic green bacteria. Int J Syst Bacteriol 26:74–75Google Scholar
  69. Van de PY, De Wachter R (1997) Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput Appl Biosci 13:227–230Google Scholar
  70. Wu D, Hugenholtz P, Mavromatis K et al (2009a) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056–1060PubMedCrossRefGoogle Scholar
  71. Wu D, Raymond J, Wu M et al (2009b) Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS ONE 4:e4207PubMedCrossRefGoogle Scholar
  72. Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE (2000) Molecular evidence for the early evolution of photosynthesis. Science 289:1724–1730PubMedCrossRefGoogle Scholar
  73. Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A (2010) Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria. Int J Syst Evol Microbiol 60:1794–1801PubMedCrossRefGoogle Scholar
  74. Yamada T, Sekiguchi Y, Hanada S et al (2006) Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56:1331–1340PubMedCrossRefGoogle Scholar
  75. Yan J, Rash BA, Rainey FA, Moe WM (2009) Detection and quantification of Dehalogenimonas and “Dehalococcoides” populations via PCR-based protocols targeting 16S rRNA genes. Appl Environ Microbiol 75:7560–7564PubMedCrossRefGoogle Scholar
  76. Yarza P, Ludwig W, Euzeby J et al (2010) Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291–299PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Radhey S. Gupta
    • 1
  • Pranay Chander
    • 1
  • Sanjan George
    • 1
  1. 1.Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonCanada

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