EMAN RESEARCH PUBLISHING | <p>Genomic Fingerprinting Using Highly Repetitive Sequences to Differentiate Close Cyanobacterial Strains</p>
Microbial and anti-microbial compound biology
RESEARCH ARTICLE   (Open Access)

Genomic Fingerprinting Using Highly Repetitive Sequences to Differentiate Close Cyanobacterial Strains

Rezvan Shokraei aHossein Fahimi aSaúl Blanco bBahareh Nowruzi c*

+ Author Affiliations

Microbial Bioactives 2(1) 068-075 https://doi.org/10.25163/microbbioacts.21015A2624310119

Submitted: 12 December 2018  Revised: 31 January 2019  Published: 24 January 2019 

Abstract

Background: Cyanobacterial taxonomy has experimented considerable changes due to the exploration of previously uninvestigated regions as well as the introduction of molecular tools. Challenges arose when strains collected from agricultural areas, salt waters and dry limestone did not reveal remarkable morphological differences and had a high level of similarity in the phylogeny of 16S rDNA gene sequences. The aim of the present investigation was to fingerprint members of the genera Calothrix and Nostoc based on the repetitive DNA sequences, as molecular markers for the detection of phylogenetic affinities and molecular diversity. Methods: In this research, through a polyphasic approach, the differences in morphological and genotypic features of different strains were investigated. Bacteria free cyanobacterial clones were prepared followed by morphological characterization, genomic DNA extraction and PCR with 16S rRNA, ERIC, STRR1a and HIP primers. Then the phylogenetic analyses of partial 16S rRNA genes and fingerprints were performed. Results: The results showed each marker producing unique and strain-specific banding pattern, thus highlighting the efficiency of this technique in the assessment of proximity between closely related cyanobacterial strains isolated from different climatic/geographic regions and habitats. Conclusions: This case is the first documented genomic fingerprinting from seven close cyanobacterial strains in Iran.

Keywords: Fingerprinting, Repetitive DNA fragments, Enterobacterial repetitive intergenic consensus (ERIC), Highly iterated palindrome, Close cyanobacteria.

References

Abony, M., Banik A., Shishir M. A., Akter N. J., Uddin M. E., Datta S. (2018). Physico-chemical Characterization of Indigenous Streptomyces and Influence of pH on Antimicrobial Activity. Microbial Bioactives, 1(2), 059-067.

https://doi.org/10.25163/microbbioacts.12009A3010021118

Akoijam, C., & Singh, A. K. (2011). Molecular typing and distribution of filamentous heterocystous cyanobacteria isolated from two distinctly located regions in North-Eastern India. World Journal of Microbiology and Biotechnology27(9), 2187-2194.

https://doi.org/10.1007/s11274-011-0684-8

Cavalier-Smith, T. (2002). The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International journal of systematic and evolutionary microbiology, 52(2), 297-354.
https://doi.org/10.1099/00207713-52-2-297
PMid:11931142

Delaye, L., & Moya, A. (2011). Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes. Mobile Genetic Elements1(3), 159-168.

https://doi.org/10.4161/mge.1.3.18300
PMid:22312590 PMCid:PMC3271550

Desikachary, T.V. Cyanophyta, (Indian Council of Agricultural Research New Delhi, 1959).

Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research32(5), 1792-1797.

https://doi.org/10.1093/nar/gkh340
PMid:15034147 PMCid:PMC390337

Elhai, J. (2015). Highly Iterated Palindromic sequences (HIPs) and their relationship to DNA methyltransferases. Life5(1), 921-948.

https://doi.org/10.3390/life5010921
PMid:25789551 PMCid:PMC4390886

Ezhilarasi, A., & An, N. (2010). Fingerprinting of repetitive DNA sequences in the genus Anabaena using PCR-based techniques. African Journal of Microbiology Research4(8), 590-597.

Gould, S. B., Waller, R. F., & McFadden, G. I. (2008). Plastid evolution. Annual Review of Plant Biology59, 491-517.

https://doi.org/10.1146/annurev.arplant.59.032607.092915
PMid:18315522

Gugger, M. F., & Hoffmann, L. (2004). Polyphyly of true branching cyanobacteria (Stigonematales). International Journal of Systematic and Evolutionary Microbiology54(2), 349-357.

https://doi.org/10.1099/ijs.0.02744-0
PMid:15023942

Helm, R. F., Huang, Z., Edwards, D., Leeson, H., Peery, W., & Potts, M. (2000). Structural characterization of the released polysaccharide of desiccation-tolerant Nostoc communeDRH-1. Journal of Bacteriology182(4), 974-982.

https://doi.org/10.1128/JB.182.4.974-982.2000
PMid:10648523 PMCid:PMC94373

Hill, D. R., Peat, A., & Potts, M. (1994). Biochemistry and structure of the glycan secreted by desiccation-tolerantNostoc commune (Cyanobacteria). Protoplasma182(3-4), 126-148.

https://doi.org/10.1007/BF01403474

Howard-Azzeh, M., Shamseer, L., Schellhorn, H. E., & Gupta, R. S. (2014). Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives. Photosynthesis Research122(2), 171-185.

https://doi.org/10.1007/s11120-014-0020-x
PMid:24917519

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. Microbiology148(2), 481-496.

https://doi.org/10.1099/00221287-148-2-481
PMid:11832512

Kaushik, P., Chauhan, A., Chauhan, G., & Goyal, P. (2009). Antibacterial potential and UV-HPLC analysis of laboratory-grown culture of Anabaena variabilis. International Journal of Food Safety11, 11-18.

Komárek J and Johansen JR. (2014) Filamentous cyanobacteria. In Freshwater Algae of North America (Second Edition). Elsevier, pp. 135-235.

Komárek, J. (2010). Recent changes (2008) in cyanobacteria taxonomy based on a combination of molecular background with phenotype and ecological consequences (genus and species concept). Hydrobiologia639(1), 245-259.

https://doi.org/10.1007/s10750-009-0031-3

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, p. 1130, Springer Spektrum Berlin, Heidelberg.

Laguerre, G., Mavingui, P., Allard, M. R., Charnay, M. P., Louvrier, P., Mazurier, S. I., ... & Amarger, N. (1996). Typing of rhizobia by PCR DNA fingerprinting and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: application to Rhizobium leguminosarum and its different biovars. Applied and Environmental Microbiology62(6), 2029-2036.

PMid:8787401 PMCid:PMC167981

Liaimer, A., Jensen, J. B., & Dittmann, E. (2016). A genetic and chemical perspective on symbiotic recruitment of cyanobacteria of the genus Nostoc into the host plant Blasia pusilla L. Frontiers in Microbiology7, 1693.

https://doi.org/10.3389/fmicb.2016.01693

Lyra, C., Laamanen, M., Lehtimäki, J. M., 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. International Journal of Systematic and Evolutionary Microbiology55(2), 555-568.

https://doi.org/10.1099/ijs.0.63288-0
PMid:15774625

Muralitharan, G., & Thajuddin, N. (2011). Rapid differentiation of phenotypically and genotypically similar Synechococcus elongatus strains by PCR fingerprinting. Biologia66(2), 238-243.

https://doi.org/10.2478/s11756-011-0003-8

Neilan, B. A., Saker, M. L., Fastner, J., Törökné, A., & Burns, B. P. (2003). Phylogeography of the invasive cyanobacterium Cylindrospermopsis raciborskii. Molecular Ecology12(1), 133-140.

https://doi.org/10.1046/j.1365-294X.2003.01709.x
PMid:12492883

Nguyen, L. T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2014). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution32(1), 268-274.

https://doi.org/10.1093/molbev/msu300
PMid:25371430 PMCid:PMC4271533

Nilsson, M., Bergman, B., & Rasmussen, U. (2000). Cyanobacterial diversity in geographically related and distant host plants of the genus Gunnera. Archives of Microbiology173(2), 97-102.

https://doi.org/10.1007/s002039900113
PMid:10795680

Nowruzi, B., Khavari-Nejad, R. A., Sivonen, K., Kazemi, B., Najafi, F., & Nejadsattari, T. (2012). Identification and toxigenic potential of a Nostoc sp. Algae27(4), 303-313.

https://doi.org/10.4490/algae.2012.27.4.303

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 Letters29, 199-211.

https://doi.org/10.1016/j.phytol.2018.12.011

Nowruzi, B., Blanco, S., & Nejadsattari, T. (2018). Chemical and Molecular Evidences for the Poisoning of a Duck by Anatoxin-a, Nodularin and Cryptophycin at the Coast of Lake Shoormast (Mazandaran Province, Iran). International Journal on Algae20(4).

https://doi.org/10.1615/InterJAlgae.v20.i4.30

Orcutt, K. M., Rasmussen, U., Webb, E. A., Waterbury, J. B., Gundersen, K., & Bergman, B. (2002). Characterization of Trichodesmium spp. by genetic techniques. Applied and Environmental Microbiology68(5), 2236-2245.

https://doi.org/10.1128/AEM.68.5.2236-2245.2002
PMid:11976093 PMCid:PMC127538

Prabina, B. J., Kumar, K., & Kannaiyan, S. (2005). DNA amplification fingerprinting as a tool for checking genetic purity of strains in the cyanobacterial inoculum. World Journal of Microbiology and Biotechnology21(5), 629-634.

https://doi.org/10.1007/s11274-004-3566-5

Prasanna, R., Kumar, R., Sood, A., Prasanna, B. M., & Singh, P. K. (2006). Morphological, physiochemical and molecular characterization of Anabaena strains. Microbiological Research161(3), 187-202.

https://doi.org/10.1016/j.micres.2005.08.001
PMid:16765835

Prasanna, R., Babu, S., Rana, A., Kabi, S. R., Chaudhary, V., Gupta, V., ... & Pal, R. K. (2013). Evaluating the establishment and agronomic proficiency of cyanobacterial consortia as organic options in wheat–rice cropping sequence. Experimental Agriculture49(3), 416-434.

https://doi.org/10.1017/S001447971200107X

Rasmussen, U., & Svenning, M. M. (1998). Fingerprinting of cyanobacteria based on PCR with primers derived from short and long tandemly repeated repetitive sequences. Applied and Environmental Microbiology64(1), 265-272.

PMid:16349487 PMCid:PMC124704

Rippka, R., Deruelles, J., Waterbury, J. B., Herdman, M., & Stanier, R. Y. (1979). Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Microbiology111(1), 1-61.

https://doi.org/10.1099/00221287-111-1-1

Rodriguez-Barradas, M. C., Hamill, R. J., Houston, E. D., Georghiou, P. R., Clarridge, J. E., Regnery, R. L., & Koehler, J. E. (1995). Genomic fingerprinting of Bartonella species by repetitive element PCR for distinguishing species and isolates. Journal of Clinical Microbiology33(5), 1089-1093.

PMid:7615711 PMCid:PMC228110

Sánchez-Baracaldo, P., Ridgwell, A., & Raven, J. A. (2014). A neoproterozoic transition in the marine nitrogen cycle. Current Biology24(6), 652-657.

https://doi.org/10.1016/j.cub.2014.01.041
PMid:24583016

Schirrmeister, B. E., Gugger, M., & Donoghue, P. C. (2015). Cyanobacteria and the Great Oxidation Event: evidence from genes and fossils. Palaeontology58(5), 769-785.

https://doi.org/10.1111/pala.12178https://doi.org/10.1111/pala.12193

PMid:26924853 PMCid:PMC4755140

Selvakumar, G., & Gopalaswamy, G. (2008). PCR based fingerprinting of Westiellopsis cultures with short tandemly repeated repetitive (STRR) and highly iterated palindrome (HIP) sequences. Biologia63(3), 283-288.

https://doi.org/10.2478/s11756-008-0065-4

Shih, P. M., Wu, D., Latifi, A., Axen, S. D., Fewer, D. P., Talla, E., Herdman, M. (2013). Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proceedings of the National Academy of Sciences110(3), 1053-1058.

https://doi.org/10.1073/pnas.1217107110
PMid:23277585 PMCid:PMC3549136

Shirkey, B., McMaster, N. J., Smith, S. C., Wright, D. J., Rodriguez, H., Jaruga, P., ... & Potts, M. (2003). Genomic DNA of Nostoc commune (Cyanobacteria) becomes covalently modified during long-term (decades) desiccation but is protected from oxidative damage and degradation. Nucleic Acids Research31(12), 2995-3005.

https://doi.org/10.1093/nar/gkg404
PMid:12799425 PMCid:PMC162238

Shishir, M. A., Pervin, S., Sultana, M., Khan, S. N., & Hoq, M. M. (2015). Genetic Diversity of Indigenous Bacillus thuringiensis Strains by RAPD-PCR to Combat Pest Resistance. Bt Research, 6(8), 1–16.

https://doi.org/10.5376/bt.2015.06.0008

Smith, J. K., Parry, J. D., Day, J. G., & Smith, R. J. (1998). A PCR technique based on the Hipl interspersed repetitive sequence distinguishes cyanobacterial species and strains. Microbiology144(10), 2791-2801.

https://doi.org/10.1099/00221287-144-10-2791
PMid:9802020

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 and Environmental Microbiology69(9), 5157-5169.

https://doi.org/10.1128/AEM.69.9.5157-5169.2003
PMid:12957897 PMCid:PMC194958

Teaumroong, N., Innok, S., Chunleuchanon, S., & Boonkerd, N. (2002). Diversity of nitrogen-fixing cyanobacteria under various ecosystems of Thailand: I. Morphology, physiology and genetic diversity. World Journal of Microbiology and Biotechnology18(7), 673-682.

https://doi.org/10.1023/A:1016812116538

Thajuddin, N., Muralitharan, G., Sundaramoorthy, M., Ramamoorthy, R., Ramachandran, S., Akbarsha, M. A., & Gunasekaran, M. (2010). Morphological and genetic diversity of symbiotic cyanobacteria from cycads. Journal of Basic Microbiology50(3), 254-265.

https://doi.org/10.1002/jobm.200900343
PMid:20473963

Uyeda, J. C., Harmon, L. J., & Blank, C. E. (2016). A comprehensive study of cyanobacterial morphological and ecological evolutionary dynamics through deep geologic time. PloS One11(9), e0162539.

https://doi.org/10.1371/journal.pone.0162539
PMid:27649395 PMCid:PMC5029880

 

Valerio, E., Chambel, L., Paulino, S., Faria, N., Pereira, P., & Tenreiro, R. (2009). Molecular identification, typing and traceability of cyanobacteria from freshwater reservoirs. Microbiology155(2), 642-656.

https://doi.org/10.1099/mic.0.022848-0
PMid:19202113

Walter, J. M., Coutinho, F. H., Dutilh, B. E., Swings, J., Thompson, F. L., & Thompson, C. C. (2017). Ecogenomics and taxonomy of Cyanobacteria phylum. Frontiers in Microbiology8, 2132.

https://doi.org/10.3389/fmicb.2017.02132

Wilson, K. M., Schembri, M. A., Baker, P. D., & Saint, C. P. (2000). Molecular characterization of the toxic cyanobacterium Cylindrospermopsis raciborskii and design of a species-specific PCR. Applied and Environmental Microbiology66(1), 332-338.

https://doi.org/10.1128/AEM.66.1.332-338.2000
PMid:10618244 PMCid:PMC91826

Zheng, W. W., Nilsson, M., Bergman, B., & Rasmussen, U. (1999). Genetic diversity and classification of cyanobacteria in different Azolla species by the use of PCR fingerprinting. Theoretical and Applied Genetics99(7-8), 1187-1193.

https://doi.org/10.1007/s001220051323

Zheng, W., Song, T., Bao, X., Bergman, B., & Rasmussen, U. (2002). High cyanobacterial diversity in coralloid roots of cycads revealed by PCR fingerprinting. FEMS Microbiology Ecology40(3), 215-222.

https://doi.org/10.1111/j.1574-6941.2002.tb00954.x

PMid:19709229

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