DNA analyses of a private collection of microbial green algae contribute to a better understanding of microbial diversity

BMC Research Notes

Ryo Hoshina¹ 

[1] Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, 526-0829 Nagahama, Shiga, Japan

关键词: Species delimitation;    Private collection;    Microbial diversity;    Internal transcribed spacer 2 (ITS2);    Green algae;   

Others  :  1129985
DOI  :  10.1186/1756-0500-7-592

 received in 2014-04-11, accepted in 2014-08-27,  发布年份 2014

【 摘 要 】

Background

DNA comparison is becoming the leading approach to the analysis of microbial diversity. For eukaryotes, the internal transcribed spacer 2 (ITS2) has emerged as a conspicuous molecule that is useful for distinguishing between species. Because of the small number of usable ITS data in GenBank, ITS2 sequence comparisons have only been used for limited taxa. However, major institutions with planktonic algal culture collections have now released small subunit (SSU) to ITS rDNA sequence data for their collections. This development has uplifted the level of molecular systematics for these algae.

Results

Forty-three strains of green algae isolated from German inland waters were investigated by using SSU-ITS rDNA sequencing. The strains were isolated through the direct plating method. Many of the strains went extinct during the years of culture. Thus, it could be expected that the surviving strains would be common, vigorous species. Nevertheless, 12 strains did not match any known species for which rDNA sequences had been determined. Furthermore, the identity of one strain was uncertain even at the genus level.

Conclusions

The aforementioned results show that long-forgotten and neglected collections may be of great significance in understanding microbial diversity, and that much work still needs to be done before the diversity of freshwater green algae can be fully described.

【 授权许可】

   
2014 Hoshina; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Adl SM, Leander BS, Simpson AGB, Archibald JM, Anderson OR, Bass D, Bowser SS, Brugerolle G, Farmer MA, Karpov S, Kolisko M, Lane CE, Lodge DJ, Mann DG, Meisterfeld R, Mendoza L, Moestrup Ø, Mozley-Standridge SE, Smirnov AV, Spiegel F: Diversity, nomenclature, and taxonomy of protists. Syst Biol 2007, 56:684-689.
• [2]Achtman M, Wagner M: Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol 2008, 6:431-40.
• [3]Huss VAR, Sogin ML: Phylogenetic position of some Chlorella species within the chlorococcales based upon complete small-subunit ribosomal RNA sequences. J Mol Evol 1990, 31:432-442.
• [4]Huss VAR, Frank C, Hartmann EC, Hirmer M, Kloboucek A, Seidel BM, Wenzeler P, Kessler E: Biochemical taxonomy and molecular phylogeny of the genus Chlorella sensu lato (Chlorophyta). J Phycol 1999, 35:587-598.
• [5]Ustinova I, Krienitz L, Huss VAR: Closteriopsis acicularis (G. M. Smith) Belcher et Swale is a fusiform alga closely related to Chlorella kessleri Fott et Nováková (Chlorophyta, Trebouxiophyceae). Eur J Phycol 2001, 36:341-351.
• [6]Wolf M, Krienitz L, Hepperle D: Phylogenetic position of Actinastrum hantzschii Lagerheim 1882 (Chlorophyta, Trebouxiophyceae). Algol Stud 2002, 104:59-67.
• [7]Krienitz L, Hegewald E, Hepperle D, Huss VAR, Rohr T, Wolf M: Phylogenetic relationship of Chlorella and Parachlorella gen. nov. (Chlorophyta, Trebouxiophyceae). Phycologia 2004, 43:529-542.
• [8]Pröschold T, Bock C, Luo W, Krienitz L: Polyphyletic distribution of bristle formation in Chlorellaceae: Micractinium, Diacanthos, Didymogenes and Hegewaldia gen. nov. (Trebouxiophyceae, Chlorophyta). Phycol Res 2010, 58:1-8.
• [9]Krienitz L, Bock C, Kotut K, Pröschold T: Genotypic diversity of Dictyosphaerium–morphospecies (Chlorellaceae, Trebouxiophyceae) in African inland waters, including the description of four new genera. Fottea 2012, 12:231-253.
• [10]Musters W, Boon K, van der Sande CA, van Heerikhuizen H, Planta RJ: Functional analysis of transcribed spacers of yeast ribosomal DNA. EMBO J 1990, 9:2989-2996.
• [11]Hadjiolova KV, Normann A, Cavaillé J, Soupéne E, Mazan S, Hadjiolov AA, Bachellerie J-P: Processing of truncated mouse or human rRNA transcribed from ribosomal minigenes transfected into mouse cells. Mol Cell Biol 1994, 14:4044-4056.
• [12]Schultz J, Maisel S, Gerlach D, Muller T, Wolf M: A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 2005, 11:361-364.
• [13]Chen S, Yao H, Han J, Liu C, Song J, Shi L, Zhu Y, Ma X, Gao T, Pang X, Luo K, Li Y, Li X, Jia X, Lin Y, Leon C: Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 2010, 5:e8613.
• [14]Coleman AW: The significance of a coincidence between evolutionary landmarks found in mating affinity and a DNA sequence. Protist 2000, 151:1-9.
• [15]Müller T, Philippi N, Dandekar T, Schultz J, Wolf M: Distinguishing species. RNA 2007, 13:1469-1472.
• [16]Fawley MW, Fawley KP, Buchheim MA: Molecular diversity among communities of freshwater microchlorophytes. Microbial Ecol 2004, 48:489-499.
• [17]Fawley MW, Fawley KP, Owen HA: Diversity and ecology of small coccoid green algae from Lake Itasca, Minnesota, USA, including Meyerella planktonica, gen. et sp. nov. Phycologia 2005, 44:35-48.
• [18]Lewis LA, Lewis PO: Unearthing the molecular phylodiversity of desert soil green algae (Chlorophyta). Syst Biol 2005, 54:936-947.
• [19]De Wever A, Leliaert F, Verleyen E, Vanormelingen P, Van der Gucht K, Hodgson DA, Sabbe K, Vyverman W: Hidden levels of phylodiversity in Antarctic green algae: further evidence for the existence of glacial refugia. Proc R Soc B 2009, 276:3591-3599.
• [20]Hosoya H, Kimura K, Matsuda S, Kitaura M, Takahashi T, Kosaka T: Symbiotic algae-free strains of the green paramecium Paramecium bursaria produced by herbicide paraquat. Zool Sci 1995, 12:807-810.
• [21]Ichimura T: Sexual cell division and conjugation-papilla formation in sexual reproduction of Closterium strigosum. In Proceedings of the Seventh International Seaweed Symposium: 1971; Tokyo Edited by Nishizawa K, Arasaki S, Chihara M, Hirose H, Nakamura V, Tsuchiya Y. 1971, 208-214.
• [22]Nakayama T, Watanabe S, Mitsui K, Uchida H, Inouye I: The phylogenetic relationship between the Chlamydomonadales and Chlorococcales inferred from 18S rDNA sequence data. Phycol Res 1996, 44:47-55.
• [23]Hoshina R, Kato Y, Kamako S, Imamura N: Genetic evidence of “American” and “European” type symbiotic algae of Paramecium bursaria Ehrenberg. Plant Biol 2005, 7:526-532.
• [24]Hoshina R, Kamako S, Imamura N: Phylogenetic position of endosymbiotic green algae in Paramecium bursaria Ehrenberg from Japan. Plant Biol 2004, 6:447-453.
• [25]White TJ, Bruns T, Lee S, Taylor J: Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols: a guide to methods and application. Edited by Innis M, Gelfand D, Sninsky J, White T. San Diego: Academic Press; 1990:315-322.
• [26]Hoshina R: Analysis of an intron intervening the SSU rDNA of Chlorella sp. T-24-5, a photobiont of Paramecium bursaria. Jpn J Protozool 2012, 45:17-27.
• [27]Hoshina R, Imamura N: Multiple origins of the symbioses in Paramecium bursaria. Protist 2008, 159:53-63.
• [28]Krienitz L, Bock C, Nozaki H, Wolf M: SSU rRNA gene phylogeny of morphospecies affiliated to the bioassay alga “Selenastrum capricornutum” recovered the polyphyletic origin of crescent-shaped Chlorophyta. J Phycol 2011, 47:880-893.
• [29]Marin B: Nested in the Chlorellales or independent class? Phylogeny and classification of the Pedinophyceae (Viridiplantae) revealed by molecular phylogenetic analyses of complete nuclear and plastid-encoded rRNA operons. Protist 2012, 163:778-805.
• [30]Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace M, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
• [31]Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR: The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002, 3:2. BioMed Central Full Text
• [32]Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739.
• [33]Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
• [34]Hegewald E, Bock C, Krienitz L: A phylogenetic study on Scenedesmaceae with the description of a new species of Pectinodesmus and the new genera Verrucodesmus and Chodatodesmus (Chlorophyta, Chlorophyceae). Fottea 2013, 13:149-164.
• [35]Eliáš M, Němcová Y, Škaloud P, Neustupa J, Kaufnerová V, Šejnohová L: Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore. Int J Syst Evol Microbiol 2010, 60:1224-1235.
• [36]Hoshina R, Fujiwara Y: Molecular characterization of Chlorella cultures of the NIES culture collection with description of Micractinium inermum sp. nov., Didymogenes sphaerica sp. nov., and Didymogenes soliella sp. nov. (Chlorellaceae, Trebouxiophyceae). Phycol Res 2013, 61:124-132.
• [37]Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415.
• [38]Krienitz L, Ustinova I, Friedl T, Huss VAR: Traditional generic concepts versus 18S rRNA gene phylogeny in the green algal family Selenastraceae (Chlorophyceae, Chlorophyta). J Phycol 2001, 37:852-865.
• [39]Fawley MW, Dean ML, Dimmer SK, Fawley KP: Evaluating the morphospecies concept in the Selenastraceae (Chlorophyceae, Chlorophyta). J Phycol 2005, 42:142-154.
• [40]Friedl T, O’Kelly CJ: Phylogenetic relationships of green algae assigned to the genus Planophila (Chlorophyta): evidence from 18S rDNA sequence data and ultrastructure. Eur J Phycol 2002, 37:373-384.
• [41]Deason TR, Silva PC, Watanabe S, Floyd GL: Taxonomic status of the species of the green algal genus Neochloris. Pl Syst Evol 1991, 177:213-219.
• [42]McManus HA, Lewis LA: Molecular phylogenetics, morphological variation and colony-form evolution in the family Hydrodictyaceae (Sphaeropleales, Chlorophyta). Phycologia 2005, 44:582-595.
• [43]Keller A, Schleicher T, Förster F, Ruderisch B, Dandekar T, Müller T, Wolf M: ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC Evol Biol 2008, 8:218. BioMed Central Full Text
• [44]Fucikova K, Lewis LA: Intersection of Chlorella, Muriella and Bracteacoccus: resurrecting the genus Chromochloris KOL et CHODAT (Chlorophyceae, Chlorophyta). Fottea 2012, 12:83-93.
• [45]Markert SM, Müller T, Koetschan C, Friedl T, Wolf M: ‘Y’ Scenedesmus (Chlorophyta, Chlorophyceae): the internal transcribed spacer 2 rRNA secondary structure re-revisited. Plant Biol 2012, 14:987-996.
• [46]Booton GC, Floyd GL, Fuerst PA: Multiple group I introns detected in the nuclear small subunit rDNA of the autosporic green alga Selenastrum capricornutum. Curr Genet 2004, 46:228-234.
• [47]Hegewald E, Wolf M, Keller A, Friedl T, Krienitz L: ITS2 sequence–structure phylogeny in the Scenedesmaceae with special reference to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella and Pectinodesmus. Phycologia 2010, 49:325-335.
• [48]Johnson JL, Fawley MW, Fawley KP: The diversity of Scenedesmus and Desmodesmus (Chlorophyceae) in Itasca State Park, Minnesota, USA. Phycologia 2007, 46:214-229.
• [49]Fawley MW, Fawley KP, Hegewald E: Taxonomy of Desmodesmus serratus (Chlorophyceae, Chlorophyta) and related taxa on the basis of morphological and DNA sequence data. Phycologia 2011, 50:23-56.
• [50]Fawley MW, Fawley KP, Hegewald E: Desmodesmus baconii (Chlorophyta), a new species with double rows of arcuate spines. Phycologia 2013, 52:565-572.
• [51]Krienitz L, Bock C: Present state of the systematics of planktonic coccoid green algae of inland waters. Hydrobiologia 2012, 698:295-326.
• [52]Luo W, Pflugmacher S, Pröschold T, Walz N, Krienitz L: Genotype versus phenotype variability in Chlorella and Micractinium (Chlorophyta, Trebouxiophyceae). Protist 2006, 157:315-333.
• [53]Bock C, Pröschold T, Krienitz L: Two new Dictyosphaerium-morphotype lineages of the Chlorellaceae (Trebouxiophyceae): Heynigia gen. nov. and Hindakia gen. nov. Eur J Phycol 2010, 45:267-277.
• [54]Bock C, Krienitz L, Pröschold T: Taxonomic reassessment of the genus Chlorella (Trebouxiophyceae) using molecular signatures (barcodes), including description of seven new species. Fottea 2011, 11:293-312.
• [55]Bock C, Pröschold T, Krienitz L: Updating the genus Dictyosphaerium and description of Mucidosphaerium gen. nov. (Trebouxiophyceae) based on morphological and molecular data. J Phycol 2011, 47:638-652.
• [56]Luo W, Pröschold T, Bock C, Krienitz L: Generic concept in Chlorella-related coccoid green algae (Chlorophyta, Trebouxiophyceae). Plant Biol 2010, 12:545-553.
• [57]Hoshina R, Iwataki M, Imamura N: Chlorella variabilis and Micractinium reisseri sp. nov. (Chlorellaceae, Trebouxiophyceae): Redescription of the endosymbiotic green algae of Paramecium bursaria (Peniculia, Oligohymenophorea) in the 120th year. Phycol Res 2010, 58:188-201.
• [58]Finlay BJ: Global dispersal of free-living microbial eukaryote species. Science 2002, 296:1061-1063.
• [59]Coleman AW: Microbial eukaryote species. Science 2002, 297:337.