Phylogenetic study of Aliinostoc species (Cyanobacteria) using pc-igs, nifH and mcy as markers for investigation of horizontal gene transfer


  • Bahareh Nowruzi



16S–23S ITS, cyanobacteria, horizontal gene transfer, molecular phylogeny, phycocyanin, ribosomal genes


Selection of genes that have not been horizontally transferred for prokaryote phylogenetic studies is regarded as a challenging task. Internal transcribed spacer of ribosomal genes (16S–23S ITS), microcystin synthetase genes (mcy), nitrogenase (nifH) and phycocyanin intergenic spacer (PC-IGS) are among the most used markers in cyanobacteria. The region of the ribosomal genes has been considered stable, whereas the nifH, mcyG and PC-IGS may have undergone horizontal transfer. To investigate the occurrence of horizontal transfer of nifH, mcyG and PC-IGS, phylogenetic trees of Aliinostoc strains Ay1375 and Me1355 were generated and compared. Phylogenetic trees based on the markers were mostly congruent for PC-IGS, indicating a common evolutionary history among ribosomal and phycocyanin genes with no evidence for horizontal transfer of PC-IGS. Phylogenetic trees constructed from the nifH and 16S rRNA genes were incongruent. Our results suggest that nifH has been transferred from one cyanobacterium to another. Moreover, the low non-synonymous/synonymous mutation ratio (Ka/Ks) was consistent with an ancient origin of the mcyG.


Bastien, C., Cardin, R., Veilleux, É., Deblois, C., Warren, A., Laurion, I., 2011. Performance evaluation of phycocyanin probes for the monitoring of cyanobacteria. Journal of Environmental Monitoring. 3, 110-8. DOI:

Brient, L., Lengronne, M., Bertrand, E., Rolland, D., Sipel, A., Steinmann, D., Baudin, I., Legeas, M., Le Rouzic, B., Bormans, M., 2008. A phycocyanin probe as a tool for monitoring cyanobacteria in freshwater bodies. Journal of Environmental Monitoring. 10, 248-55. DOI:

Chan, P.P., Lin, B.Y., Mak, A.J., Lowe, T.M., 2021. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Research, 16, 9077-96. DOI:

Dadheech, P.K., Ballot, A., Casper, P., Kotut, K., Novelo, E., Lemma, B., Pröschold, T., Krienitz, L., 2010. Phylogenetic relationship and divergence among planktonic strains of Arthrospira (Oscillatoriales, Cyanobacteria) of African, Asian and American origin deduced by 16S–23S ITS and phycocyanin operon sequences. Phycologia, 4, 361-72. DOI:

Dyble, J., Paerl, H.W., Neilan, B.A., 2002. Genetic characterization of Cylindrospermopsis raciborskii (Cyanobacteria) isolates from diverse geographic origins based on nifH and cpcBA-IGS nucleotide sequence analysis. Applied and Environmental Microbiology, 5, 2567-71. DOI:

Edgar, R.C., 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-7. DOI:

Fewer, D.P., Rouhiainen, L., Jokela, J., Wahlsten, M., Laakso, K., Wang, H., Sivonen, K., 2007. Recur- rent adenylation domain replacement in the microcystin synthetase gene cluster. BMC Evolutionary Biology, 7, 183. DOI:

Foster, R.A., Zehr, J.P., 2006. Characterization of diatom–cyanobacteria symbioses on the basis of nifH, hetR and 16S rRNA sequences. Environmental Microbiology, 11, 1913-25. DOI:

Gaby, J.C., Buckley, D.H., 2012. A comprehensive evaluation of PCR primers to amplify the nifH gene of nitrogenase. PloS One, 7, 3-6. DOI:

Gribaldo, S., Brochier, C., 2009. Phylogeny of prokaryotes: does it exist and why should we care? Research in Microbiology, 7, 513-21. DOI:

Guajardo-Leiva, S., Pedrós-Alió, C., Salgado, O., Pinto, F., Díez, B., 2018. Active crossfire between Cyanobacteria and Cyanophages in phototrophic mat communities within hot springs. Frontiers in Microbiology, 3, 20-39. DOI:

Han, D., Fan, Y., Hu, Z., 2009. An evaluation of four phylogenetic markers in Nostoc: implications for cyanobacterial phylogenetic studies at the intrageneric level. Current Microbiology, 58, 170-6. DOI:

Iteman, I., Rippka, R., de Marsac, N.T., Herdman, M., 2000. Comparison of conserved structural and regulatory domains within divergent 16S rRNA–23S rRNA spacer sequences of cyanobacteria. The GenBank accession numbers for the sequences reported in this paper are AF180968 and AF180969 for ITS-L and ITS-S, respectively. Microbiology, 146, 1275-86. DOI:

Iteman, I., Rippka, R., de Marsac, N.T., Herdman, M., 2002. rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira. The GenBank acces- sion numbers of the 16S rDNA gene sequences reported in this paper are AY038032–AY038037. Microbiology, 148, 481-96. DOI:

Johansen, J.R., Kovacik, L., Casamatta, D.A., Iková, K.F., Kastovský, J., 2011. Utility of 16S-23S ITS sequence and secondary structure for recognition of intrageneric and intergeneric limits within cyanobacterial taxa: Leptolyngbya corticola sp. nov.(Pseudanabaenaceae, Cyanobacteria). Nova Hedwigia, 92, 283. DOI:

Jungblut, A.D., Neilan, BA., 2006. Molecular identification and evolution of the cyclic peptide hepa- totoxins, microcystin and nodularin, synthetase genes in three orders of cyanobacteria. Archives of Microbiology, 185, 107-14. DOI:

Junier, P., Witzel, K.P., Hadas, O., 2007. Genetic diversity of cyanobacterial communities in Lake Kinneret (Israel) using 16S rRNA gene, psbA and ntcA sequence analyses. Aquatic Microbial Ecology, 29, 233-41. DOI:

Kabirnataj, S., Nematzadeh, G.A., Talebi, A.F., Saraf, A., Suradkar, A., Tabatabaei, M., Singh, P., 2020. Description of novel species of Aliinostoc, Desikacharya and Desmonostoc using a polyphasic approach. International Journal of Systematic and Evolutionary Microbiology, 70, 3413-26. DOI:

Komárek, J., 2016. A polyphasic approach for the taxonomy of cyanobacteria: principles and applica- tions. European Journal of Phycology, 51, 346-53. DOI:

Koonin, E.V., Makarova, K.S., Aravind, L., 2002. Horizontal gene transfer in prokaryotes: quantification and classification. Annual Review of Microbiology, 55, 709-742. DOI:

Leikoski, N., Fewer, D.P., Sivonen, K., 2009. Widespread occurrence and lateral transfer of the cyanobac- tin biosynthesis gene cluster in cyanobacteria. Applied and Environmental Microbiology, 75, 853-7. DOI:

Neilan, B.A., Jacobs, D., Blackall, L.L., Hawkins, P.R., Cox, P.T., Goodman, A.E., 1997. rRNA sequences and evolutionary relationships among toxic and nontoxic cyanobacteria of the genus Microcystis. International Journal of Systematic and Evolutionary Microbiology, 47, 693-7. DOI:

Nguyen, L.T., Schmidt, H.A., Von Haeseler, A., Minh, B.Q., 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32, 268-74. DOI:

Nowruzi, B., Blanco, S., 2019. In silico identification and evolutionary analysis of candidate genes involved in the biosynthesis methylproline genes in cyanobacteria strains of Iran. Phytochemistry Letters, 29, 199-211. DOI:

Nowruzi, B., Soares, F., 2021. Alborzia kermanshahica gen. nov., sp. nov. (Chroococcales, Cyano- bacteria), isolated from paddy fields in Iran. International Journal of Systematic and Evolutionary Microbiology, 30, 004828. DOI:

Nowruzi, B., Lorenzi, A.S., 2021. Characterization of a potentially microcystin-producing Fischerella sp. isolated from Ajigol wetland of Iran. South African Journal of Botany, 137, 423-33. DOI:

Nowruzi, B., Shalygin, S., 2021. Multiple phylogenies reveal a true taxonomic position of Dulcicalothrix alborzica sp. nov.(Nostocales, Cyanobacteria). Fottea, 21, 235-46. DOI:

Nowruzi, B., Hutárová, L., Absalón, I.B., Liu, L., 2022. A new strain of Neowestiellopsis (Hapalo- siphonaceae): first observation of toxic soil cyanobacteria from agricultural fields in Iran. BMC microbiology, 22, 1-3. DOI:

Piccin‐Santos, V., Brandão, M.M., Bittencourt‐Oliveira, M.D., 2014. Phylogenetic study of Geitlerine- ma and Microcystis (Cyanobacteria) using PC‐IGS and 16S–23S ITS as markers: investigation of horizontal gene transfer. Journal of Phycology, 50, 736-43. DOI:

Rantala, A., Fewer, D.P., Hisbergues, M., Rouhiainen, L., Vaitomaa, J., Börner, T., Sivonen, K., 2004. Phylogenetic evidence for the early evolution of microcystin synthesis. Proceedings of the National Academy of Sciences, 13, 568-73. DOI:

Rippka, R., Deruelles, J., Waterbury, JB., Herdman, M., Stanier, R.Y., 1979. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Microbiology, 111, 1-61. DOI:

Robertson, B.R., Tezuka, N., Watanabe, M.M., 2001. Phylogenetic analyses of Synechococcus strains (cyanobacteria) using sequences of 16S rDNA and part of the phycocyanin operon reveal multiple evolutionary lines and reflect phycobilin content. International Journal of Systematic and Evoluti- onary Microbiology, 51, 861-71. DOI:

Sanchis, D., Padilla, C., Del Campo, F.F., Quesada, A., Sanz-Alferez, S. 2005. Phylogenetic and morphological analyses of Microcystis strains (Cyanophyta/Cyanobacteria) from a Spanish water reservoir. Nova Hedwigia, 81,431-436. DOI:

Six, C., Thomas, JC., Garczarek, L., Ostrowski, M., Dufresne, A., Blot, N., Scanlan, D.J., Partensky, F., 2007. Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study. Genome Biology, 12, 1-22 DOI:

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. Applied Environmental Microbiology, 69, 5157–5169. DOI:

Teneva, I., Stoyanov, P., Mladenov, R., Dzhambazov, B., 2012. Molecular and phylogenetic characte- rization of two species of the genus Nostoc (Cyanobacteria) based on the cpcB-IGS-cpcA locus of the phycocyanin operon. Journal of Bioscience and Biotechnology, 1, 9-19.

Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F., Papke, R.T., 2006. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome research, 16, 1099-108. DOI:

Zuker, M., 2013. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406-15. DOI:

Yerrapragada, S., Siefert, J.L., Fox, G.E., 2009. Horizontal gene transfer in cyanobacterial signature genes. Horizontal Gene Transfer, 339-66. DOI:






Original Research Paper

How to Cite

Nowruzi, B. (2022). Phylogenetic study of Aliinostoc species (Cyanobacteria) using pc-igs, nifH and mcy as markers for investigation of horizontal gene transfer. Acta Biologica Slovenica, 65(2), 104-115.

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