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Phylogenetic Relationships of Arthrospira Strains Inferred from 16S Rrna Gene and Cpcba-IGS Sequences

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Phylogenetic Relationships of Arthrospira Strains Inferred from 16S Rrna Gene and Cpcba-IGS Sequences Research Article Algae 2012, 27(2): 75-82 http://dx.doi.org/10.4490/algae.2012.27.2.075 Open Access Phylogenetic relationships of Arthrospira strains inferred from 16S rRNA gene and cpcBA-IGS sequences Gang-Guk Choi1, Chi-Yong Ahn1 and Hee-Mock Oh1,* 1Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305- 806, Korea Arthrospira platensis and Arthrospira maxima are species of cyanobacteria used in health foods, animal feed, food additives, and fine chemicals. This study conducted a comparison of the 16S rRNA gene and cpcBA-intergenic spacer (cpcBA-IGS) sequences in Arthrospira strains from culture collections around the world. A cluster analysis divided the 10 Arthrospira strains into two main genotypic clusters, designated I and II, where Group I contained A. platensis SAG 86.79, UTEX 2340, A. maxima KCTC AG30054, and SAG 49.88, while Group II contained A. platensis PCC 9108, NIES 39, NIES 46, and SAG 257.80. However, although A. platensis PCC 9223 belonged to Group II-2 based on its cpcBA-IGS sequence, this strain also belonged to Group I based on its 16S rRNA gene sequence. Phylogenetic analyses based on the 16S rRNA gene and cpcBA-IGS sequences showed no division between A. platensis and A. maxima, plus the 16S rRNA gene and cpcBA- IGS sequence clusters did not indicate any well-defined geographical distribution, instead overlapping in a rather inter- esting way. Therefore, the current study supports some previous conclusions based on 16S rRNA gene and cpcBA-IGS sequences, which found that Arthrospira taxa are monophyletic. However, when compared with 16S rRNA sequences, cpcBA-IGS sequences may be better suited to resolve close relationships and intraspecies variability. Key Words: Arthrospira (Spirulina); cpcBA-IGS; phylogenetic analysis; 16S rRNA gene INTRODUCTION Arthrospira is a commercially important filamentous zation (FAO) (Dillon et al. 1995). Plus, it does not require cyanobacterium with an annual production estimated any chemical or physical processing in order to become at over 3,000 tons per year, the largest among microalgae digestible due to the absence of a cellulose cell wall (Pulz and Gross 2004). Found in tropical and subtropi- (Vonshak 1997b). Indeed, it can be used as feed for fish, cal regions in warm lakes with a high carbonate and bi- poultry, and farm animals (Belay 1997, Vonshak 1997a). carbonate content, and high pH and salinity (Tomaselli Originating from the taxonomic studies of cyanobacte- 1997), Arthrospira is a rich source of proteins, minerals, ria by Geitler (1932), some confusion has arisen between vitamin B12, β-carotene, and essential fatty acids, such the genera Spirulina and Arthrospira (Desikachary and as γ-linolenic acid. Owing to its high protein content of Jeeji-Bai 1996). While the 16S rRNA gene sequences of up to approximately 60-70% on a dry weight basis, the these two genera indicate that they are only distantly re- amino acids present in Arthrospira match the propor- lated (Nelissen et al. 1994, Scheldeman et al. 1999), pu- tions recommended by the Food and Agriculture Organi- tative species of Arthrospira have been recognized in the This is an Open Access article distributed under the terms of the Received April 21, 2012, Accepted May 26, 2012 Creative Commons Attribution Non-Commercial License (http://cre- Corresponding Author ativecommons.org/licenses/by-nc/3.0/) which permits unrestricted * non-commercial use, distribution, and reproduction in any medium, E-mail: [email protected] provided the original work is properly cited. Tel: +82-42-860-4321, Fax: +82-42-879-8103 Copyright © The Korean Society of Phycology 75 http://e-algae.kr pISSN: 1226-2617 eISSN: 2093-0860 Algae 2012, 27(2): 75-82 so-called ‘Spirulina’ commercial industrial field. that of the widely used 16S rRNA gene sequence (Lyra et Microscopy identification of cyanobacteria is rapid and al. 2001). sensitive. However, even with skilled and experienced op- Accordingly, the aim of this study is to clarify the di- erators, identification is sometimes uncertain. Thus, mo- versity of cultivated strains of Arthrospira using sequence lecular approaches are particularly useful in the detec- data from a highly variable DNA fragment, including a tion and identification of specific strains, especially those comparison of the phylogeny of Arthrospira strains based that are morphologically identical at the species level. on the 16S rRNA gene and cpcBA-IGS. Plus, to define and Plus, genetic identification has been used to discriminate delimit the genus Arthrospira, this study also includes nuisance species in cyanobacterial genera, including Mi- other cyanobacteria. Finally, this study attempts to iden- crocystis, Anabaena, Nodularia, and Cylindrospermopsis tify a specific molecular marker to fingerprint different (Wilmotte and Golubic 1991, Neilan et al. 1995). strains of Arthrospira and develop tools for species and Phylogenetic analyses based on the 16S rRNA gene strain identification. and cpcBA-intergenic spacer (cpcBA-IGS) take consid- erable time and effort, yet they provide certainty in the identification of genera using both the length and the se- MATERIALS AND METHODS quence of the cpcBA-IGS. In addition to 16S rRNA gene sequence analyses (Otsuka et al. 1998, Honda et al. 1999, Strains and growth conditions Turner et al. 1999), the genes encoding the major light- harvesting accessory pigment proteins, particularly the Ten Arthrospira cultures and one Spirulina culture phycocyanin operon (cpc), including the IGS between were obtained from different culture collections across cpcB and cpcA and the corresponding flanking regions the world. Table 1 shows a list of the 10 Arthrospira strains, (cpcBA-IGS), have also been targeted for phylogenetic along with their origin, culture history, and the corre- studies of cyanobacteria (Neilan et al. 1995, Barker et al. sponding DNA database accession numbers for the 16S 1999). Furthermore, to determine the phyletic relation- rRNA gene and cpcBA-IGS. The cultures were maintained ships between Arthrospira strains, a region of the phyco- in an SOT medium (Choi et al. 2003), containing per li- cyanin locus, namely cpcBA-IGS, has been sequenced, as ter 16.8 g of NaHCO3, 0.5 g of K2HPO4, 2.5 g of NaNO3, its nucleotide substitution rate is potentially higher than 1 g of K2SO4, 1 g of NaCl, 0.2 g of MgSO4·7H2O, 0.04 g of Table 1. Origins and accession numbers for Arthrospira and Spirulina strains Accession no. Strain designation Strain numbera Origin 16S rRNA gene cpcBA-IGS Arthrospira platensis NIES 39 Chad Lake, Chad DQ393279 DQ393287 NIES 46 Texcoco Lake, Mexico -b DQ393288 UTEX 2340 Natron Lake, Chad DQ393280 DQ393289 SAG 86.79 Natron Lake, Chad - DQ393291 SAG 257.80 Laguna Huacachina, Ica, Peru DQ393282 DQ393292 SAG 21.99 Walfishbay, Lagune, Namibia DQ393283 DQ393293 PCC 9108 Commericla Culture Facility, DQ393284 DQ393295 Cheng-hai, Yunnan, China PCC 9223 Lake Santa Olalla, Donana National Park, Spain DQ393285 DQ393296 Arthrospira maxima KCTC AG30054 Bangkok, Thailand DQ393281 DQ393290 SAG 49.88 Italy - DQ393294 Spirulina laxissima SAG 256.80 Lake Nakuru, Kenya DQ393278 DQ393286 cpcBA-IGS, cpcBA-intergenic spacer. aNIES, National Institute for Environmental Studies Collection, Tsukuba, Ibaraki, Japan; UTEX, Culture Collection of Algae at the University of Texas at Austin, Austin, TX, USA; SAG, Sammlung von Algenkulturen der Universität Göttingen, Germany; PCC, Pasteur Culture Collection of Cyanobac- terial Strains, Paris, France; KCTC, Korean Collection for Type Cultures, Daejeon, Korea. b-: not amplified. http://dx.doi.org/10.4490/algae.2012.27.2.075 76 Choi et al. Phylogenetic Analyses of Arthrospira Strains CaCl2·2H2O, 0.01 g of FeSO4·7H2O, 0.08 g of Na2EDTA, tree was evaluated by bootstrap analyses based on 1,000 0.03 mg of H3BO3, 0.025 mg of MnSO4·7H2O, 0.002 mg of resamplings. Due to the spacer variability, a phylogenetic ZnSO4·7H2O, 0.0079 mg of CuSO4·5H2O, and 0.0021 mg of analysis of the matrix was also performed using just the Na2MoO4·2H2O. Stock cultures of 10 mL were kept under two coding regions. Finally, an overview of the phyloge- low light (20 μmol photons m-2 s-1) and at a constant tem- netic position of Arthrospira in cyanobacteria was cre- perature of 25 ± 1°C. ated by comparing the 16S rRNA gene and cpcBA-IGS sequences to corresponding cyanobacterial sequences DNA extraction, amplification, and sequencing available in databases and the sequences obtained in this study for Spirulina laxissima SAG 256.80 and Oscillatoria The cultured strains were harvested using centrifuga- sancta NIER 10027. tion, and the genomic DNA extracted following the meth- od of Neilan et al. (1995) using lysozyme and proteinase K. The 16S rRNA gene was then amplified using the univer- RESULTS AND DISCUSSION sal primers 27F (5′-AGAGTTTGATCMTGCTGGCTCAG-3′) and 1512R (5′-GGYTACCTTGTTACGACTT-3′) (Cho and Phylogenetic tree of 16S rRNA gene Giovannoni 2003). The PCR products were purified using a Qiagen QIAquick PCR purification column and cloned Near-complete 16S rRNA gene sequences were deter- using a pDrive vector (Qiagen, Hilden, Germany). The mined for 7 Arthrospira strains and 1 Spirulina strain re- cpcBA-IGS was amplified using primers located within ceived from culture collections across the world. A phy- the coding region of cpcB and cpcA, respectively, where logenetic tree was then reconstructed using a NJ analysis the forward primer was CPC1F (5′-GGC KGC YTG YYT based on aligning the 8 sequences with Escherichia coli GCG YGA CAT GGA-3′) and the reverse primer was CPC1R K-12 and Bacillus subtilis as the outgroup (Fig. 1). The (5 -AAR CGN CCT TGR GWA TCD GC-3′) (Kim et al. 2006). corrected sequence alignment, providing the basis of the The amplified fragments (annealing temperature 55°C) phylogenetic analyses, corresponded to positions 8-1512 ʹ were purified using a Qiagen QIAquick PCR purification according to the E.
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