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Cho HS, Lee J. Taxonomic reinvestigation of the genus Tetradesmus (Scenedesmaceae; Sphaeropleales) based on morphological characteristics and chloroplast genomes. FRONTIERS IN PLANT SCIENCE 2024; 15:1303175. [PMID: 38419779 PMCID: PMC10899504 DOI: 10.3389/fpls.2024.1303175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
The genus Tetradesmus (Scenedesmaceae; Sphaeropleales) comprises one of the most abundant green algae in freshwater environments. It includes morphologically diverse species that exhibit bundle-like, plane-arranged coenobia, and unicells, because several different Scenedesmus-like groups were integrated into this genus based on phylogenetic analysis. Nevertheless, there is no clear information regarding the phylogenetic relationship of Tetradesmus species, determined using several marker genes, because of low phylogenetic support and insufficient molecular data. Currently, genome information is available from diverse taxa, which could provide high-resolution evolutionary relationships. In particular, phylogenetic studies using chloroplast genomes demonstrated the potential to establish high-resolution phylogenetic relationships. However, only three chloroplast genomes are available from the genus Tetradesmus. In this study, we newly generated 9 chloroplast genomes from Tetradesmus and constructed a high-resolution phylogeny using a concatenated alignment of 69 chloroplast protein sequences. We also report one novel species (T. lancea), one novel variety (T. obliquus var. spiraformis), and two novel formae (T. dissociatus f. oviformis, T. obliquus f. rectilineare) within the genus Tetradesmus based on morphological characteristics (e.g., cellular arrangements and coenobial types) and genomic features (e.g., different exon-intron structures in chloroplast genomes). Moreover, we taxonomically reinvestigated the genus Tetradesmus based on these results. Altogether, our study can provide a comprehensive understanding of the taxonomic approaches for investigating this genus.
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Affiliation(s)
- Hyeon Shik Cho
- Department of Oceanography, Kyungpook National University, Daegu, Republic of Korea
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, Republic of Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu, Republic of Korea
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Wang J, Zhang Q, Chen N, Chen J, Zhou J, Li J, Wei Y, Bu D. A new Desmodesmus sp. from the Tibetan Yamdrok Lake. PLoS One 2022; 17:e0275799. [PMID: 36206243 PMCID: PMC9544026 DOI: 10.1371/journal.pone.0275799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/23/2022] [Indexed: 11/19/2022] Open
Abstract
Revegetation of exposed sub-soil, while a desirable recovery strategy, often fails due to extreme soil chemical properties, such as low organic matter and pH levels. Microalgae play a key role in maintaining water quality in the lakes and rivers on the Qinghai-Tibet plateau. Plateau microalgae have extensive application prospects in environmental purification, biotechnology, medicine and cosmetics, food industry, and renewable energy. To identify the high biomass of microalgae present in nature, microalgae with the greatest biomass were screened from natural water samples through filtration, pre-culture, and plate scribing separation. Following identification via 18S rRNA sequencing as for the Desmodesmus sp., we constructed a neighbor-joining phylogenetic tree. The novel Desmodesmus sp. from the Tibetan Yamdrok Lake were identified through polyphasic taxonomy. Simultaneously, the sequence of the experimental samples and the target species were shown different following the identification and analysis of SNP and InDel loci. The light-absorbing properties of plateau Desmodesmus sp. have been investigated previously. The characteristic absorption peak of Desmodesmus sp. on the plateau was measured at 689 nm in the visible spectrum using full wavelength scanning with a UV-Vis spectrophotometer. For Desmodesmus sp. which is prone to settling in the process of amplification culture. By monitoring the change trend of total nitrogen, total phosphorus, pH and electrical conductivity in algae solution system, we determined that the logarithmic growth phase and the best transfer window of Desmodesmus sp. were at 15-20 days. This study can provide basic research methods for the study of microalgae in high altitude areas, and lay a foundation for the later study and application of microalgae.
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Affiliation(s)
- Jinhu Wang
- College of Science, Tibet University, Lhasa City, Tibet Autonomous Region, P. R. China
| | - Qiangying Zhang
- College of Science, Tibet University, Lhasa City, Tibet Autonomous Region, P. R. China
| | - Naijiang Chen
- Lianyungang Food and Drug Inspection and Testing Center, Lianyungang City, Jiangsu Province, P. R. China
| | - Junyu Chen
- College of Science, Tibet University, Lhasa City, Tibet Autonomous Region, P. R. China
| | - Jinna Zhou
- College of Science, Tibet University, Lhasa City, Tibet Autonomous Region, P. R. China
| | - Jing Li
- College of Science, Tibet University, Lhasa City, Tibet Autonomous Region, P. R. China
| | - Yanli Wei
- College of Science, Tibet University, Lhasa City, Tibet Autonomous Region, P. R. China
| | - Duo Bu
- College of Science, Tibet University, Lhasa City, Tibet Autonomous Region, P. R. China
- * E-mail:
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Shetty P, Farkas A, Pap B, Hupp B, Ördög V, Bíró T, Varga T, Maróti G. Comparative and phylogenomic analysis of nuclear and organelle genes in cryptic Coelastrella vacuolata MACC-549 green algae. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Ballesteros I, Terán P, Guamán-Burneo C, González N, Cruz A, Castillejo P. DNA barcoding approach to characterize microalgae isolated from freshwater systems in Ecuador. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.1920296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Isabel Ballesteros
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | - Paulina Terán
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | | | - Nory González
- AgroScience & Food Research Group, Universidad de las Américas, Quito, Ecuador
| | - Alejandra Cruz
- Ingeniería en Biotecnología. Facultad de Ingenierías y Ciencias Aplicadas, Universidad de las Américas, Quito, Ecuador
| | - Pablo Castillejo
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
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Revision of Coelastrella (Scenedesmaceae, Chlorophyta) and first register of this green coccoid microalga for continental Norway. World J Microbiol Biotechnol 2020; 36:149. [PMID: 32914262 PMCID: PMC7496060 DOI: 10.1007/s11274-020-02897-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/12/2020] [Indexed: 11/26/2022]
Abstract
A terrestrial green microalga was isolated at Ås, in Akershus County, Norway. The strain corresponded to a coccoid chlorophyte. Morphological characteristics by light and electron microscopy, in conjunction with DNA amplification and sequencing of the 18 s rDNA gene and ITS sequences, were used to identify the microalgae. The characteristics agree with those of the genus Coelastrella defined by Chodat, and formed a sister group with the recently described C. thermophila var. globulina. Coelastrella is a relatively small numbered genus that has not been observed in continental Norway before; there are no previous cultures available in collections of Norwegian strains. Gas chromatography analyses of the FAME-derivatives showed a high percentage of polyunsaturated fatty acids (44–45%) especially linolenic acid (C18:3n3; 30–34%). After the stationary phase, the cultures were able to accumulate several carotenoids as neoxanthin, pheophytin a, astaxanthin, canthaxanthin, lutein, and violaxanthin. Due to the scarcity of visual characters suitable for diagnostic purposes and the lack of DNA sequence information, there is a high possibility that species of this genus have been neglected in local environmental studies, even though it showed interesting properties for algal biotechnology.
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A Review of Algae-Based Produced Water Treatment for Biomass and Biofuel Production. WATER 2020. [DOI: 10.3390/w12092351] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Produced water (PW), the largest waste stream generated in oil and gas industries, has the potential to be a harmless product rather than being a waste. Biological processes using microorganisms have proven useful to remediate PW contaminated by petroleum hydrocarbons, complex organic chemicals, and solvents. In particular, the bioremediation of PW using algae is an eco-friendly and low-cost approach due to algae’s ability to utilize certain pollutants as nutrient sources. Therefore, the utilization of PW as an algal growth medium has a great potential to eliminate chemicals from the PW and minimize the large volumes of freshwater needed for cultivation. Although several reviews describing the bioremediation of PW have been published, to the best of our knowledge, no review has exclusively focused on the algae-based PW treatment. Therefore, the present review is dedicated to filling this gap by portraying the many different facets of the algae cultivation in PW. Several algal species that are known to thrive in a wide range of salinity and the critical steps for their cultivation in hypersaline PW have been identified. Overall, this comprehensive review highlights the PW bioremediation using algae and brings attention to utilizing PW to grow biomass that can be processed to generate biofuels and useful bioproducts.
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Pediludiella daitoensis gen. et sp. nov. (Scenedesmaceae, Chlorophyceae), a large coccoid green alga isolated from a Loxodes ciliate. Sci Rep 2020; 10:628. [PMID: 31959793 PMCID: PMC6971069 DOI: 10.1038/s41598-020-57423-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
Freshwater protists often harbor unicellular green algae within their cells. In ciliates, possibly because of large host cell sizes and the small size of algal coccoids, a single host cell typically contains more than a hundred algal cells. While surveying such algae-bearing protists on Minami Daito Jima Island in Japan, we found a green Loxodes ciliate (Loxodida, Karyorelictea) that contained one or two dozens of very large coccoid algae. We isolated one of these algae and analyzed its characteristics in detail. A small subunit (SSU) rDNA phylogeny indicated Pseudodidymocystis species (Scenedesmaceae, Chlorophyceae) to be the taxon closest to the alga, although it was clearly separated from this by 39 or more different sites (inclusive of gaps). SSU rRNA structure analyses indicated that these displacements included eight compensatory base changes (CBCs) and seven hemi-CBCs. We therefore concluded that this alga belongs to a separate genus, and described it as Pediludiella daitoensis gen. et sp. nov. The shape of the isolated and cultured P. daitoensis was nearly spherical and reached up to 30 µm in diameter. Chloroplasts were arranged peripherally and often split and elongated. Cells were often vacuolated and possessed a net-like cytoplasm that resembled a football (soccer ball) in appearance, which was reflected in the genus name.
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Wang Q, Song H, Liu X, Liu B, Hu Z, Liu G. Morphology and molecular phylogeny of coccoid green algae Coelastrella sensu lato (Scenedesmaceae, Sphaeropeales), including the description of three new species and two new varieties. JOURNAL OF PHYCOLOGY 2019; 55:1290-1305. [PMID: 31411734 DOI: 10.1111/jpy.12915] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/01/2019] [Indexed: 05/16/2023]
Abstract
The genus Coelastrella was established by Chodat (Bull. Soc. Bot. Geneve, 13 [1922] 66), and was characterized as being unicellular or in few-celled aggregations with many longitudinal ribs on the cell wall. Many species of this genus showed strong ability to accumulate carotenoids and oils, so they have recently attracted much attention from researchers due to its potential applicability in the energy and food industries. In this study, a total of 23 strains of Coelastrella were sampled from China, and three new species and two new varieties were described: C. thermophila sp. nov., C. yingshanensis sp. nov., C. tenuitheca sp. nov., C. thermophila var. globulina var. nov., C. rubescens var. oocystiformis var. nov. Besides 18S rDNA and ITS2 sequences, we have newly sequenced the tufA gene marker for this taxon. Phylogenetic analysis combined with morphological studies revealed four morphotypes within the Coelastrella sensu lato clade, which contained the morphotype of original Coelastrella, original Scotiellopsis, Asterarcys, and morphotype of C. vacuolata and C. tenuitheca sp. nov. The relationships between morphological differences and phylogenic diversity based on different markers were discussed. Our results support that 18S rDNA was too conserved to be used a species-specific or even a genus-specific marker in this clade. The topology of tufA gene-based phylogenetic tree had a better match with the morphological findings.
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Affiliation(s)
- Qinghua Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100039, P. R. China
| | - Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Xudong Liu
- School of Life Science, Shanxi University, Taiyuan, 030006, P. R. China
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100039, P. R. China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China
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He L, Wang Z, Lou S, Lin X, Hu F. The complete chloroplast genome of the green algae Hariotina reticulata (Scenedesmaceae, Sphaeropleales, Chlorophyta). Genes Genomics 2018; 40:543-552. [DOI: 10.1007/s13258-018-0652-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/26/2017] [Indexed: 10/18/2022]
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Characterization and classification of highly productive microalgae strains discovered for biofuel and bioproduct generation. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.01.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Sciuto K, Lewis LA, Verleyen E, Moro I, La Rocca N. Chodatodesmus australis sp. nov. (Scenedesmaceae, Chlorophyta) from Antarctica, with the emended description of the genus Chodatodesmus, and circumscription of Flechtneria rotunda gen. et sp. nov. JOURNAL OF PHYCOLOGY 2015; 51:1172-1188. [PMID: 26987011 DOI: 10.1111/jpy.12355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
The family Scenedesmaceae is a taxonomically complicated group due to its simple morphology, high phenotypic plasticity, and the presence of cryptic taxa. Over the years several taxonomic revisions, based on molecular data, affected the family. Here, we describe a new scenedesmacean species from Antarctica, Chodatodesmus australis, based on phylogenetic analyses of data from nuclear (ITS2 spacer, 18S rDNA), and plastid (rbcL, tufA) markers. Morphological (LM and SEM) and ultrastructural (TEM) observations, carried out both on the holotype of C. australis and on the generitype of Chodatodesmus, allow us to emend the original generic description of this genus. Our molecular and phylogenetic data also reveal the existence of a new monotypic genus, Flechtneria, inside the family Scenedesmaceae and lead to the taxonomic reassignment of some microalgal strains available in International Culture Collections to new taxa. Of the considered genomic regions, the tufA gene was the easiest to amplify and sequence and it showed the highest phylogenetic signal, even if the number of sequences already available for this marker in the public databases was considerably lower than for the other chosen loci. The rbcL gene also provided good phylogenetic signal, but its amplification and sequencing were generally more problematic. The nuclear markers gave lower phylogenetic signals, but the 18S rDNA allowed distinction at the genus level and the ITS2 spacer had the advantage that secondary structures could be considered in the analyses. The use of more than one molecular locus is suggested to obtain reliable results in the characterization of scenedesmacean strains.
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Affiliation(s)
- Katia Sciuto
- Department of Biology, University of Padova, via U. Bassi 58/B, Padova, 35131, Italy
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, 06269-3043, USA
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281 - S8, Gent, 9000, Belgium
| | - Isabella Moro
- Department of Biology, University of Padova, via U. Bassi 58/B, Padova, 35131, Italy
| | - Nicoletta La Rocca
- Department of Biology, University of Padova, via U. Bassi 58/B, Padova, 35131, Italy
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Gorelova OA, Baulina OI, Solovchenko AE, Chekanov KA, Chivkunova OB, Fedorenko TA, Lobakova ES. Similarity and diversity of the Desmodesmus spp. microalgae isolated from associations with White Sea invertebrates. PROTOPLASMA 2015; 252:489-503. [PMID: 25189657 DOI: 10.1007/s00709-014-0694-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/22/2014] [Indexed: 05/16/2023]
Abstract
Similarity and diversity of the phenotype and nucleotide sequences of certain genome loci among the single-celled microalgae isolated from White Sea benthic invertebrates were studied to extend the knowledge of oxygenic photoautotrophs forming microbial communities associated with animals. We compared four Desmodesmus isolates (1Hp86E-2, 1Pm66B, 3Dp86E-1, 2Cl66E) from the sponge Halichondria panicea, trochophore larvae of the polychaete Phyllodoce maculata, and the hydroids Dynamena pumila and Coryne lovenii, respectively. The microalgae appeared to be very similar featuring the phenotypic and genetic traits characteristics of unicellular representatives of the genus Desmodesmus. At the same time, isolates from different animal species displayed certain differences in (i) the epistructure morphology; (ii) type and number of the inclusions such as interthylakoid starch grains and cytoplasmic oil bodies and (iii) fatty acid composition; in Desmodesmus sp. 1Hp86E-2, these differences were most pronounced. Phylogenetic analysis based on ITS1-5.8S rRNA-ITS2 and rbcL sequences showed that all isolates studied differ from known classified representatives of Desmodesmus combining a deletion in the conservative 5.8S rRNA gene and long AC-microsatellite repeats in the ITS1 whereas 1Hp86E-2 represented a distinct branch within this group.
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Affiliation(s)
- Olga A Gorelova
- Department of Bioengineering, Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia
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Chokshi K, Pancha I, Trivedi K, George B, Maurya R, Ghosh A, Mishra S. Biofuel potential of the newly isolated microalgae Acutodesmus dimorphus under temperature induced oxidative stress conditions. BIORESOURCE TECHNOLOGY 2015; 180:162-71. [PMID: 25600013 DOI: 10.1016/j.biortech.2014.12.102] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 12/29/2014] [Accepted: 12/30/2014] [Indexed: 05/08/2023]
Abstract
Lack of control over temperature is one of the major issues in large scale cultivation of microalgae. Therefore, it is important to evaluate the effects of cultivation temperature on the growth and physiology of microalgae. In the present study, freshwater microalgae Acutodesmus dimorphus was grown at different temperature in continuous and two stage cultivation. Results revealed that during continuous cultivation A. dimorphus grows better at 35°C than at 25°C and 38°C. At 35°C, A. dimorphus produced 22.7% lipid (containing 59% neutral lipid) and 33.7% carbohydrate along with 68% increase in biomass productivity (23.53mg/L/day) compared to 25°C grown culture. Stress biomarkers like reactive oxygen species, antioxidant enzymes like catalase and ascorbate peroxidase and lipid peroxidation were also lowest in 35°C grown culture which reveals that A. dimorphus is well acclimatized at 35°C.
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Affiliation(s)
- Kaumeel Chokshi
- Discipline of Salt & Marine Chemicals, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Imran Pancha
- Discipline of Salt & Marine Chemicals, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Khanjan Trivedi
- Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Discipline of Wasteland Research, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Basil George
- Discipline of Salt & Marine Chemicals, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Rahulkumar Maurya
- Discipline of Salt & Marine Chemicals, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Arup Ghosh
- Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Discipline of Wasteland Research, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India
| | - Sandhya Mishra
- Discipline of Salt & Marine Chemicals, CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India; Academy of Scientific & Innovative Research (AcSIR), CSIR - Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India.
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Hoshina R. DNA analyses of a private collection of microbial green algae contribute to a better understanding of microbial diversity. BMC Res Notes 2014; 7:592. [PMID: 25182710 PMCID: PMC4167140 DOI: 10.1186/1756-0500-7-592] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Ryo Hoshina
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura 1266, 526-0829 Nagahama, Shiga, Japan.
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Škaloud P, Kalina T, Nemjová K, De Clerck O, Leliaert F. Morphology and Phylogenetic Position of the Freshwater Green Microalgae Chlorochytrium (Chlorophyceae) and Scotinosphaera (Scotinosphaerales, ord. nov., Ulvophyceae). JOURNAL OF PHYCOLOGY 2013; 49:115-129. [PMID: 27008394 DOI: 10.1111/jpy.12021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/22/2012] [Indexed: 06/05/2023]
Abstract
The green algal family Chlorochytriaceae comprises relatively large coccoid algae with secondarily thickened cell walls. Despite its morphological distinctness, the family remained molecularly uncharacterized. In this study, we investigated the morphology and phylogenetic position of 16 strains determined as members of two Chlorochytriaceae genera, Chlorochytrium and Scotinosphaera. The phylogenetic reconstructions were based on the analyses of two data sets, including a broad, concatenated alignment of small subunit rDNA and rbcL sequences, and a 10-gene alignment of 32 selected taxa. All analyses revealed the distant relation of the two genera, segregated in two different classes: Chlorophyceae and Ulvophyceae. Chlorochytrium strains were inferred in two distinct clades of the Stephanosphaerinia clade within the Chlorophyceae. Whereas clade A morphologically fits the description of Chlorochytrium, the strains of clade B coincide with the circumscription of the genus Neospongiococcum. The Scotinosphaera strains formed a distinct and highly divergent clade within the Ulvophyceae, warranting the recognition of a new order, Scotinosphaerales. Morphologically, the order is characterized by large cells bearing local cell wall thickenings, pyrenoid matrix dissected by numerous anastomosing cytoplasmatic channels, sporogenesis comprising the accumulation of secondary carotenoids in the cell periphery and almost simultaneous cytokinesis. The close relationship of the Scotinosphaerales with other early diverging ulvophycean orders enforces the notion that nonmotile unicellular freshwater organisms have played an important role in the early diversification of the Ulvophyceae.
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Affiliation(s)
- Pavel Škaloud
- Charles University in Prague, Faculty of Science, Department of Botany, Benátská 2, 128 01, Prague 2, Czech Republic
| | - Tomáš Kalina
- Charles University in Prague, Faculty of Science, Department of Botany, Benátská 2, 128 01, Prague 2, Czech Republic
| | - Katarína Nemjová
- Charles University in Prague, Faculty of Science, Department of Botany, Benátská 2, 128 01, Prague 2, Czech Republic
| | - Olivier De Clerck
- Phycology Research Group, Biology Department, Ghent University, Krijgslaan 281 S8, 9000, Ghent, Belgium
| | - Frederik Leliaert
- Phycology Research Group, Biology Department, Ghent University, Krijgslaan 281 S8, 9000, Ghent, Belgium
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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 BIOLOGY (STUTTGART, GERMANY) 2012; 14:987-996. [PMID: 22639929 DOI: 10.1111/j.1438-8677.2012.00576.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. It is possible to simultaneously infer alignments and phylogenies on the primary sequence and the secondary structure information. For the internal transcribed spacer 2 (ITS2), a phylogenetic RNA transcript marker, two different structure conformations (I or Y shape for helix I) were published for Scenedesmaceae, and a third appeared in the ITS2 database. We contrast the effects on phylogenetic tree reconstruction of different structure sets for a small scenedesmacean subset, using neighbour-joining, maximum parsimony and, for the first time, maximum likelihood, on sequence-structure alignments. Generally our study supports inclusion of secondary structure information. However, we found that any of the three structure conformations is equally fit for phylogenetic studies, but prefer the I shape for helix I. Moreover, our results enable us to give general recommendations on how to build a phylogenetic tree using ITS2 sequence-structure alignments, including different methods to obtain the secondary structures. Thus, we hope to provide a valuable contribution not only for scenedesmacean ITS2 phylogeny, but also for other approaches using RNA transcript markers.
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Affiliation(s)
- S M Markert
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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Hodač L, Hallmann C, Rosenkranz H, Faßhauer F, Friedl T. Molecular Evidence for the Wide Distribution of Two Lineages of Terrestrial Green Algae (Chlorophyta) over Tropics to Temperate Zone. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/795924] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phylogenetic analyses of 18S rDNA sequences from environmental clones and culture strains revealed a widespread distribution of two subaerial green algal lineages, Jenufa and Xylochloris, recently described from rainforests in southeast Asia. A new lineage of Jenufa (Chlorophyceae), most closely related to or even conspecific with J. minuta, was formed by sequences of European origin. Two more lineages of Jenufa were formed by three additional sequences from Ecuador and Panama. The other lineage was a close relative of Xylochloris irregularis (Trebouxiophyceae), probably representing a new species of the genus and distinct from the only so far described species, X. irregularis. It comprised two distinct clades each containing almost identical sequences from Germany and Ecuador. Analyses of the new sequences for both genera allowed to presume a preference of J. minuta to subaerial growth on rock or artificial hard substrates combined with a remarkable adaptation to extended periods of darkness, whereas Xylochloris may preferably occur on tree bark or in the soil.
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Affiliation(s)
- Ladislav Hodač
- Experimental Phycology and Culture Collection of Algae (SAG), Georg August University Göttingen, Untere Karspüle 2a, 37073 Göttingen, Germany
| | - Christine Hallmann
- Experimental Phycology and Culture Collection of Algae (SAG), Georg August University Göttingen, Untere Karspüle 2a, 37073 Göttingen, Germany
| | - Helen Rosenkranz
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Fabian Faßhauer
- Experimental Phycology and Culture Collection of Algae (SAG), Georg August University Göttingen, Untere Karspüle 2a, 37073 Göttingen, Germany
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae (SAG), Georg August University Göttingen, Untere Karspüle 2a, 37073 Göttingen, Germany
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Lang I, Hodac L, Friedl T, Feussner I. Fatty acid profiles and their distribution patterns in microalgae: a comprehensive analysis of more than 2000 strains from the SAG culture collection. BMC PLANT BIOLOGY 2011; 11:124. [PMID: 21896160 PMCID: PMC3175173 DOI: 10.1186/1471-2229-11-124] [Citation(s) in RCA: 212] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 09/06/2011] [Indexed: 05/02/2023]
Abstract
BACKGROUND Among the various biochemical markers, fatty acids or lipid profiles represent a chemically relatively inert class of compounds that is easy to isolate from biological material. Fatty acid (FA) profiles are considered as chemotaxonomic markers to define groups of various taxonomic ranks in flowering plants, trees and other embryophytes. RESULTS The fatty acid profiles of 2076 microalgal strains from the culture collection of algae of Göttingen University (SAG) were determined in the stationary phase. Overall 76 different fatty acids and 10 other lipophilic substances were identified and quantified. The obtained FA profiles were added into a database providing information about fatty acid composition. Using this database we tested whether FA profiles are suitable as chemotaxonomic markers. FA distribution patterns were found to reflect phylogenetic relationships at the level of phyla and classes. In contrast, at lower taxonomic levels, e.g. between closely related species and even among multiple isolates of the same species, FA contents may be rather variable. CONCLUSION FA distribution patterns are suitable chemotaxonomic markers to define taxa of higher rank in algae. However, due to their extensive variation at the species level it is difficult to make predictions about the FA profile in a novel isolate.
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Affiliation(s)
- Imke Lang
- Georg-August-University, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Göttingen, Germany
- Cyano-Biofuels GmbH, Magnussstrasse 11, 12489 Berlin, Germany
| | - Ladislav Hodac
- Georg-August-University, Albrecht-von-Haller-Institute for Plant Sciences, Department of Experimental Phycology and Culture Collection of Algae in Göttingen (EPSAG), Göttingen, Germany
| | - Thomas Friedl
- Georg-August-University, Albrecht-von-Haller-Institute for Plant Sciences, Department of Experimental Phycology and Culture Collection of Algae in Göttingen (EPSAG), Göttingen, Germany
| | - Ivo Feussner
- Georg-August-University, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Göttingen, Germany
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Němcová Y, Eliáš M, Škaloud P, Hodač L, Neustupa J. JENUFA GEN. NOV.: A NEW GENUS OF COCCOID GREEN ALGAE (CHLOROPHYCEAE, INCERTAE SEDIS) PREVIOUSLY RECORDED BY ENVIRONMENTAL SEQUENCING(1). JOURNAL OF PHYCOLOGY 2011; 47:928-938. [PMID: 27020027 DOI: 10.1111/j.1529-8817.2011.01009.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The diversity of eukaryotic microorganisms is far from fully described, as indicated by the vast number of unassigned genotypes retrieved by environmental sequencing or metagenomics. We isolated several strains of unicellular green algae from algal biofilms growing on tree bark in a Southeast Asian tropical rainforest and determined them to be relatives of an unidentified lineage of environmental 18S rDNA sequences, thus uncovering its cellular identity. Light, confocal, and electron microscope observations and sequencing the 18S rRNA gene revealed that the strains represent two different species within an apparently new genus, described here as Jenufa gen. nov. Both species formed minute coccoid cells with an irregular globular outline, a smooth cell wall, and a single parietal chloroplast without a pyrenoid. The two species, described herein as J. perforata and J. minuta, differed in chloroplast morphology and cell wall structure. Phylogenetic analyses of 18S rRNA gene sequences showed a firm relationship between the two species and placed the Jenufa lineage in an unresolved position within the CS clade (Chlamydomonadales + Sphaeropleales) of the class Chlorophyceae, although possible affinities to the genus Golenkinia were suggested both by maximum-likelihood (ML) and Bayesian methods. Furthermore, two almost identical environmental 18S rDNA sequences from an endolithic microbial community occurring in dolomite rock in the central Alps turned out to be specifically related to, yet apparently distinct from, the sequence of J. minuta, indicating the existence of an undescribed Jenufa species occurring in the temperate zone.
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Affiliation(s)
- Yvonne Němcová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Slezská Ostrava, Czech RepublicDepartment of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
| | - Marek Eliáš
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Slezská Ostrava, Czech RepublicDepartment of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Slezská Ostrava, Czech RepublicDepartment of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
| | - Ladislav Hodač
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Slezská Ostrava, Czech RepublicDepartment of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
| | - Jiří Neustupa
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Slezská Ostrava, Czech RepublicDepartment of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
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