Plant Systematics and Evolution

, Volume 302, Issue 10, pp 1381–1394 | Cite as

New species of Nostoc (cyanobacteria) isolated from Pune, India, using morphological, ecological and molecular attributes

  • Prashant Singh
  • Zaid M. Shaikh
  • Lira A. Gaysina
  • Archana Suradkar
  • Upasona Samanta
Original Article


Filamentous cyanobacterium (strain NE-PS) isolated from a freshwater body in Pune, India, is being described as new species of the polyphyletic genus Nostoc. Phenotypic and molecular characterizations were performed, and the combined results validated the strain as a new species. Careful observations of the filaments, the presence of a distinct sheath throughout the length of the trichome, prominent differences in the shape and dimensions of the vegetative cells, heterocytes and the akinetes provided reliable morphological signals that the strain differed from rest of the closely related species. Sequencing of the 16S rRNA gene showed 98.66 % sequence similarity with Nostoc linckia, while rbcL and psbA sequencing showed 97 and 94 % similarities with Nostoc sp. PCC 7906 and Nostoc punctiforme PCC 73102, respectively, while the nifD gene sequence similarity was found to be 96 % with N. punctiforme Ind35 and Desmonostoc muscorum. The PC-IGS region was sequenced and concatenated cpcB, IGS and cpcA regions indicated the closest similarity with Nostoc linckia PACC 5085 at 96 %. Subsequent phylogenetic analyses gave a strong pattern of distinct clustering in case of all the molecular markers. The phenotypic, genetic and phylogenetic observations prove conclusively that the strain NE-PS is a new species in the genus Nostoc with the name proposed being Nostoc punensis, sp. nov.


Cyanobacteria Evolution Phylogeny Systematics 



We thank the Director NCCS for facilities and encouragement. This work was supported by the Department of Biotechnology (DBT; Grant no. BT/PR/0054/NDB/52/94/2007), the Government of India, under the project ‘Establishment of Microbial Culture Collection’. L.A. Gaysina is thankful to the Russian Foundation for Basic Research in frame of projects 15-29-05893 ofr-i. We are immensely grateful to Mr. Yunir Gabidullin for helping us in preparation of all the plates and in arrangement of all the images.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

606_2016_1337_MOESM1_ESM.pdf (405 kb)
Online Resource 1 A general view of the trichomes of the strain NE-PS (40X). (PDF 405 kb)
606_2016_1337_MOESM2_ESM.pdf (449 kb)
Online Resource 2 Loosely arranged trichomes with a view of the vegetative cells, heterocytes (both terminal and intercalary) (40X). (PDF 448 kb)
606_2016_1337_MOESM3_ESM.pdf (466 kb)
Online Resource 3 Arrangement of trichomes with the constrictions between cells being visible noticeably (40X). (PDF 466 kb)
606_2016_1337_MOESM4_ESM.pdf (423 kb)
Online Resource 4 Trichome arrangement with terminal heterocytes having one and two polar nodules (40X). (PDF 423 kb)
606_2016_1337_MOESM5_ESM.pdf (1.4 mb)
Online Resource 5 Plate showing general view of routine trichomes with characteristic features of the strain NE-PS (40X) (PDF 1442 kb)
606_2016_1337_MOESM6_ESM.pdf (419 kb)
Online Resource 6 1—trichome with intercalary heterocytes (40X); 2—trichomes with terminal heterocytes (40X). (PDF 418 kb)
606_2016_1337_MOESM7_ESM.pdf (434 kb)
Online Resource 7 Neighbor Joining tree (NJ) tree of the strain NE-PS based on the 16S rRNA gene. (PDF 434 kb)
606_2016_1337_MOESM8_ESM.pdf (427 kb)
Online Resource 8 Maximum parsimony tree (MP) tree of the strain NE-PS based on the 16S rRNA gene. (PDF 426 kb)
606_2016_1337_MOESM9_ESM.pdf (425 kb)
Online Resource 9 Neighbor Joining tree (NJ) tree of the strain NE-PS based on the rbcL gene. (PDF 425 kb)
606_2016_1337_MOESM10_ESM.pdf (419 kb)
Online Resource 10 Maximum parsimony tree (MP) tree of the strain NE-PS based on the rbcL gene. (PDF 418 kb)
606_2016_1337_MOESM11_ESM.pdf (412 kb)
Online Resource 11 Neighbor Joining tree (NJ) tree of the strain NE-PS based on the psbA gene. (PDF 412 kb)
606_2016_1337_MOESM12_ESM.pdf (404 kb)
Online Resource 12 Maximum parsimony tree (MP) tree of the strain NE-PS based on the psbA gene. (PDF 404 kb)
606_2016_1337_MOESM13_ESM.pdf (416 kb)
Online Resource 13 Neighbor Joining tree (NJ) tree of the strain NE-PS based on the nifD gene. (PDF 416 kb)
606_2016_1337_MOESM14_ESM.pdf (411 kb)
Online Resource 14 Maximum parsimony tree (MP) tree of the strain NE-PS based on the nifD gene. (PDF 410 kb)
606_2016_1337_MOESM15_ESM.pdf (414 kb)
Online Resource 15 Neighbor Joining tree (NJ) tree of the strain NE-PS based on the PC-IGS region. (PDF 414 kb)
606_2016_1337_MOESM16_ESM.pdf (410 kb)
Online Resource 16 Maximum parsimony tree (MP) tree of the strain NE-PS based on the PC-IGS region. (PDF 409 kb)


  1. Anagnostidis K, Komárek J (1985) Modern approach to the classification system of the cyanophytes 1. Introduction. Algol Stud 38:291–302Google Scholar
  2. Anagnostidis K, Komárek J (1988) Modern approach to the classification system of the cyanophytes 3. Oscillatoriales. Algol Stud 50:327–472Google Scholar
  3. Anagnostidis K, Komárek J (1990) Modern approach to the classification system of the cyanophytes 5. Stigonematales. Algol Stud 86:1–74Google Scholar
  4. Andreote APD, Vaz MGMV, Genuário DB, Barbiero L, Rezende-Filho AT, Fiore MF (2014) Nonheterocytous cyanobacteria from Brazilian saline-alkaline lakes. J Phycol 50:675–684CrossRefPubMedGoogle Scholar
  5. Belknap WR, Hazelkorn R (1987) Cloning and light regulation of expression of the phycocyanin operon of the cyanobacterium Anabaena. EMBO J 6:871–884PubMedPubMedCentralGoogle Scholar
  6. Bornet É, Flahault C (1888) Revision des Nostocacées hétérocystées contenues dans les principaux herbiers de France (quatrième et dernier fragment). Ann Sci Nat Bot 7:177–262Google Scholar
  7. Büdel B, Kauff F (2012) Blue-green algae. In: Frey W (ed) Syllabus of plant families, Engler’s syllabus der Pflanzenfamilien, part VI. Borntraeger, Stuttgart, pp 5–39Google Scholar
  8. Desikachary TV (1959) Cyanophyta. ICAR monographs on algae, New DelhiGoogle Scholar
  9. Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410CrossRefGoogle Scholar
  10. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Molec Evol 17:368–376CrossRefPubMedGoogle Scholar
  11. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  12. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specified tree topology. Syst Zool 20:406–416CrossRefGoogle Scholar
  13. Fox GE, Wisotzkey JD, Jurtshuk P Jr (1992) How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170CrossRefPubMedGoogle Scholar
  14. Gascuel O, Steel M (2006) Neighbor-joining revealed. Molec Biol Evol 23:1997–2000CrossRefPubMedGoogle Scholar
  15. Genuário DB, Correa DM, Komárek J, Fiore MF (2013) Characterization of freshwater benthic biofilmforming Hydrocoryne (Cyanobacteria) isolates from Antarctica. J Phycol 49:1142–1153CrossRefPubMedGoogle Scholar
  16. Gugger M, Hoffmann L (2004) Polyphyly of true branching cyanobacteria (Stigonematales). Int J Syst Evol Microbiol 54:349–357CrossRefPubMedGoogle Scholar
  17. Gugger M, Lyra C, Henrikso P, Coute A, Humbert JF, Sivonen K (2002) Phylogenetic comparison of the cyanobacterial genera Anabaena and Aphanizomenon. Int J Syst Evol Microbiol 52:1867–1880PubMedGoogle Scholar
  18. Hašler P, Dvořák P, Johansen JR, Kitner M, Ondřej V, Poulíčková A (2012) Morphological and molecular study of epipelic filamentous genera Phormidium, Microcoleus and Geitlerinema (Oscillatoriales, Cyanophyta/Cyanobacteria). Fottea 12:341–356Google Scholar
  19. Henson BJ, Watson LE, Barnum SR (2002) Molecular differentiation of the heterocystous cyanobacteria, Nostoc and Anabaena, based on complete nifD sequences. Curr Microbiol 45:161–164CrossRefPubMedGoogle Scholar
  20. Henson BJ, Hesselbrock SM, Watson LE, Barnum SR (2004) Molecular phylogeny of the heterocystous cyanobacteria (subsections IV and V) based on nifD. Int J Syst Evol Microbiol 54:493–497CrossRefPubMedGoogle Scholar
  21. Hrouzek P, Ventura S, Lukesova A, Mugnai MA, Turicchia S, Komârek J (2005) Diversity of soil Nostoc strains: phylogenetic and phenotypic variability. Algol Stud 117:16–122CrossRefGoogle Scholar
  22. Imhoff JF, Madigan MT (2007) International committee on systematics of prokaryotes; subcommittee on the taxonomy of phototrophic bacteria. Int J Syst Evol Microbiol 57:1169–1171CrossRefGoogle Scholar
  23. Iteman I, Rippka R, Tandeau de Marsac N, Herdman M (2002) rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira. Microbiol 148:481–496CrossRefGoogle Scholar
  24. Johansen JR, Casamatta DA (2005) Recognizing cyanobacterial diversity through adoption of a new species paradigm. Algol Stud 117:71–93CrossRefGoogle Scholar
  25. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132CrossRefGoogle Scholar
  26. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721CrossRefPubMedGoogle Scholar
  27. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Molec Evol 16:111–120CrossRefPubMedGoogle Scholar
  28. Komárek J (2013) Cyanoprokaryota. 3. Heterocytous genera. In: Büdel B, Gärtner G, Krienitz L, Schagerl M (eds) Süswasserflora von Mitteleuropa/freshwater flora of Central Europe. Springer, HeidelbergGoogle Scholar
  29. Komárek J (2016) A polyphasic approach for the taxonomy of cyanobacteria: principles and applications. Eur J Phycol 51:346–353. doi: 10.1080/09670262.2016.1163738 CrossRefGoogle Scholar
  30. Komárek J, Anagnostidis K (1986) Modern approach to the classification system of the cyanophytes 2. Chroococcales. Algol Stud 43:157–226Google Scholar
  31. Komárek J, Anagnostidis K (1989) Modern approach to the classification system of the cyanophytes 4. Nostocales. Algol Stud 56:247–345Google Scholar
  32. Komárek J, Kaštovský J, Mareš J, Johansen JR (2014) Taxonomic classification of cyanoprokaryotes (cyanobacterial genera) using a polyphasic approach. Preslia 86:295–335Google Scholar
  33. Lyra C, Suomalainen S, Gugger M, Vezie C, Sundman P, Paulin L, Sivonen K (2001) Molecular characterization of planktic cyanobacteria of Anabaena, Aphanizomenon, Microcystis and Planktothrix genera. Int J Syst Evol Microbiol 51:513–526CrossRefPubMedGoogle Scholar
  34. Lyra C, Laamanen M, Lehtimaki JM, Surakka A, Sivonen K (2005) Benthic cyanobacteria of the genus Nodularia are non-toxic, without gas vacuoles, able to glide and genetically more diverse than planktonic Nodularia. Int J Syst Evol Microbiol 55:555–568CrossRefPubMedGoogle Scholar
  35. Mateo P, Perona E, Berrendero E, Leganes F, Martin M, Golubic S (2011) Life cycle as a stable trait in the evaluation of diversity of Nostoc from biofilms in rivers. FEMS Microbiol Ecol 76:185–198CrossRefPubMedGoogle Scholar
  36. Mathur M, Tuli R (1990) Cluster analysis of genes for nitrogen fixation from several diazotrophs. J Genet 69:67–78CrossRefGoogle Scholar
  37. Meeks JC, Elhai J, Thiel T, Potts M, Larimer F, Lamerdin J, Predki P, Atlas R (2001) An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium. Photosynth Res 70:85–106CrossRefPubMedGoogle Scholar
  38. Mollenhauer D (1970) Beitrage zur Kenntnis der Gattung Nostoc, I. Abh Senckenberg Naturf Ges 524:1–80Google Scholar
  39. Mollenhauer D, Bengtsson R, Lindstrøm EA (1999) Macroscopic cyanobacteria of the genus Nostoc: a neglected and endangered constituent of European inland aquatic biodiversity. Eur J Phycol 34:349–360CrossRefGoogle Scholar
  40. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New YorkGoogle Scholar
  41. Neilan BA, Jacobs D, Goodman A (1995) Genetic diversity and phylogeny of toxic cyanobacteria determined by DNA polymorphisms within the phycocyanin locus. Appl Environm Microbiol 6:3875–3883Google Scholar
  42. Pardia F, Guillemota S, Gascuela O (2010) Robustness of phylogenetic inference based on minimum evolution. Bull Math Biol 72:1820–1839CrossRefGoogle Scholar
  43. Perkerson RB, Johansen JR, Kováčik L, Brand J, Kaštovský J, Casamatta DA (2011) A unique pseudanabaenalean (Cyanobacteria) genus Nodosilinea gen. nov. based on morphological and molecular data. J Phycol 47:1397–1412CrossRefGoogle Scholar
  44. Rajaniemi P, Hrouzek P, Kaštovská K, Willame R, Rantala A, Hoffmann L, Komárek J, Sivonen K (2005a) Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria). Int J Syst Evol Microbiol 55:11–26CrossRefPubMedGoogle Scholar
  45. Rajaniemi P, Komárek J, Hrouzek P, Willame R, Kaštovská K, Hoffmann L, Sivonen K (2005b) Taxonomic consequences from the combined molecular and phenotype evaluation of selected Anabaena and Aphanizomenon strains. Algol Stud 117:371–391CrossRefGoogle Scholar
  46. Reháková K, Johansen JR, Casamatta DA, Xuesong L, Vincent J (2007) Morphological and molecular characterization of selected desert soil cyanobacteria: three species new to science including Mojavia pulchra gen. et sp. nov. Phycologia 46:481–502CrossRefGoogle Scholar
  47. Rippka R, Deruelles J, Waterbury JB, Herdman MR, Stanier RY (1979) Generic assignments, strain histories and properties of pure cultures of Cyanobacteria. J Gen Microbiol 111:1–61Google Scholar
  48. Rudi K, Skulberg OM, Jakobsen KS (1998) Evolution of cyanobacteria by exchange of genetic material among phyletically related strains. J Bacteriol 180:3453–3461PubMedPubMedCentralGoogle Scholar
  49. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molec Biol Evol 4:406–425PubMedGoogle Scholar
  50. Saker M, Moreira C, Martins J, Neilan B, Vasconcelos VM (2009) DNA profiling of complex bacterial populations: toxic cyanobacterial blooms. Appl Microbiol Biotechnol 85:237–252CrossRefPubMedGoogle Scholar
  51. Schirrmeister BE, Antonelli A, Bagheri HC (2011) The origin of multicellularity in cyanobacteria. BMC Evol Biol 11:45CrossRefPubMedPubMedCentralGoogle Scholar
  52. Shih PM, Wu D, Latifi A, Axen SD, Fewer DP, Talla E, Calteau A, Cai F, Tandeau de Marsac N, Rippka R, Herdman M, Sivonen K, Coursin T, Laurent T, Goodwin L, Nolan M, Davenport KW, Han CS, Rubin EM, Eisen JA, Woyke T, Gugger M, Kerfeld CA (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci USA 110:1053–1058CrossRefPubMedGoogle Scholar
  53. Shimada A, Yano N, Kanai S, Lewin RA, Maruyama T (2003) Molecular phylogenetic relationship between two symbiotic photo-oxygenic prokaryotes, Prochloron sp. and Synechocystis trididemni. Phycologia 42:193–197CrossRefGoogle Scholar
  54. Silva CSP, Genuário DB, Vaz MGMV, Fiore MF (2014) Phylogeny of culturable cyanobacteria from Brazilian mangroves. Syst Appl Microbiol 37:100–112CrossRefPubMedGoogle Scholar
  55. Singh P, Singh SS, Elster J, Mishra AK (2013) Molecular phylogeny, population genetics and evolution of heterocystous cyanobacteria using nifH gene sequences. Protoplasma 250:751–764CrossRefPubMedGoogle Scholar
  56. Singh P, Fatma A, Mishra AK (2015a) Molecular phylogeny and evogenomics of heterocystous cyanobacteria using rbcl gene sequence data. Ann Microbiol 65:799–807CrossRefGoogle Scholar
  57. Singh P, Singh SS, Aboal M, Mishra AK (2015b) Decoding cyanobacterial phylogeny and molecular evolution using an evonumeric approach. Protoplasma 252:519–535CrossRefPubMedGoogle Scholar
  58. Strackerbrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155Google Scholar
  59. Tamura K (1992) Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. Molec Biol Evol 9:678–687PubMedGoogle Scholar
  60. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molec Biol Evol 28:2731–2739CrossRefPubMedPubMedCentralGoogle Scholar
  61. Taton A, Grubisic S, Brambilla E, De Wit R, Wilmotte A (2003) Cyanobacterial diversity in natural and artificial microbial mats of Lake Fryxell (McMurdo dry valleys, Antarctica): a morphological and molecular approach. Appl Environ Microbiol 69:5157–5169CrossRefPubMedPubMedCentralGoogle Scholar
  62. Taton A, Grubisic S, Ertz D, Hodgson DA, Picardi R, Biondi N, Tredici M, Mainini M, Losi D, Marinelli F, Wilmotte A (2006) Polyphasic study of antarctic cyanobacterial strains. J Phycol 42:1257–1270CrossRefGoogle Scholar
  63. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  64. Turicchia S, Ventura S, Komarkova J, Komárek J (2009) Taxonomic evaluation of cyanobacterial microflora from alkaline marshes of northern Belize. 2. Diversity of oscillatorialean genera. Nova Hedwigia 89:165–200CrossRefGoogle Scholar
  65. Xia X (2013) DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Molec Biol Evol 30:1720–1728CrossRefPubMedPubMedCentralGoogle Scholar
  66. Zammit G, Billi D, Albertano P (2012) The subaerophytic cyanobacterium Oculatella subterranea (Oscillatoriales, Cyanophyceae) gen. et sp. nov.: a cytomorphological and molecular description. Eur J Phycol 47:341–354CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  • Prashant Singh
    • 1
  • Zaid M. Shaikh
    • 1
  • Lira A. Gaysina
    • 2
    • 3
  • Archana Suradkar
    • 1
  • Upasona Samanta
    • 1
  1. 1.Microbial Culture Collection (MCC)National Centre for Cell Science (NCCS)PuneIndia
  2. 2.Department of Bioecology and Biological EducationM. Akmullah Bashkir State Pedagogical UniversityUfaRussian Federation
  3. 3.All-Russian Research Institute of PhytopathologyMoscow RegionRussian Federation

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