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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Barizzone F, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 18: Suitability of taxonomic units notified to EFSA until March 2023. EFSA J 2023; 21:e08092. [PMID: 37434788 PMCID: PMC10331572 DOI: 10.2903/j.efsa.2023.8092] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023] Open
Abstract
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, no new information was found that would change the status of previously recommended QPS TUs. Of 38 microorganisms notified to EFSA between October 2022 and March 2023 (inclusive) (28 as feed additives, 5 as food enzymes, food additives and flavourings, 5 as novel foods), 34 were not evaluated because: 8 were filamentous fungi, 4 were Enterococcus faecium and 2 were Escherichia coli (taxonomic units that are excluded from the QPS evaluation) and 20 were taxonomic units (TUs) that already have a QPS status. Three of the other four TUs notified within this period were evaluated for the first time for a possible QPS status: Anaerobutyricum soehngenii, Stutzerimonas stutzeri (former Pseudomonas stutzeri) and Nannochloropsis oculata. Microorganism strain DSM 11798 has also been notified in 2015 and as its taxonomic unit is notified as a strain not a species, it is not suitable for the QPS approach. A. soehngenii and N. oculata are not recommended for the QPS status due to a limited body of knowledge of its use in the food and feed chains. S. stutzeri is not recommended for inclusion in the QPS list based on safety concerns and limited information about the exposure of animals and humans through the food and feed chains.
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Zhu J, Yu Z, He L, Jiang Y, Cao X, Song X. The molecular mechanisms and environmental effects of modified clay control algal blooms in aquacultural water. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 337:117715. [PMID: 36934499 DOI: 10.1016/j.jenvman.2023.117715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Modified clay (MC) technology is an effective method for controlling harmful algal blooms (HABs). Based on field experience, a bloom does not continue after treatment with MC, even though the residual HAB biomass accounts for 20-30% of the initial biomass. Laboratory studies using unialgal cultures have found that MC could inhibit the growth of the residual algal cells to prevent HABs. Nevertheless, the phytoplankton in field waters is diverse. Therefore, unclassified complex mechanisms may exist. To illustrate the molecular mechanisms through which MC controls HABs in the field and verify the previous laboratory findings, a series of experiments and bioinformatics analyses were conducted using bloom waters from aquacultural ponds. The results showed that a 72.29% removal efficiency of algal biomass could effectively control blooms. The metatranscriptomic results revealed that the number of downregulated genes (131,546) was greater than that of upregulated genes (24,318) at 3 h after MC addition. Among these genes, several genes related to DNA replication were downregulated; however, genes involved in DNA repair were upregulated. Metabolism-related pathways were the most significantly upregulated (q < 0.05), including photosynthesis and oxidative phosphorylation. The results also showed that MC reduced most of the biomass of the dominant phytoplankton species, likely by removing apical dominance, which increased the diversity and stability of the phytoplankton community. In addition to reducing the pathogenic bacterial density, MC reduced the concentrations of PO43- (96.22%) and SiO32- (66.77%), thus improving the aquaculture water quality, altering the phytoplankton community structure (the proportion of Diatomea decreased, and that of Chlorophyta increased), and inhibiting phytoplankton growth. These effects hindered the rapid development of large phytoplankton biomasses and allowed the community structure to remain stable, reducing HAB threats. This study illustrates the molecular mechanisms through which MC controls HABs in the field and provides a scientific method for removing HABs in aquacultural waters.
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Affiliation(s)
- Jianan Zhu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory of Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China; Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory of Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China; Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Liyan He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory of Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China; Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yuxin Jiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Xihua Cao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory of Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China; Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiuxian Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory of Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China; Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
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Ding XT, Fan Y, Jiang EY, Shi XY, Krautter E, Hu GR, Li FL. Expression of the Vitreoscilla hemoglobin gene in Nannochloropsis oceanica regulates intracellular oxygen balance under high-light. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 221:112237. [PMID: 34116318 DOI: 10.1016/j.jphotobiol.2021.112237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022]
Abstract
Nannochloropsis oceanica is widely used as a model photosynthetic chassis to produce fatty acids and carotenoid pigments. However, intense light typically causes excessive generation of reactive oxygen species (ROS) and photorespiration in microalgal cells, which results in decreased cell growth rate and unsaturated fatty acid content. In this study, the Vitreoscilla hemoglobin gene (vgb) was introduced into N. oceanica cells and expressed by using the light-harvesting complex promoter and its signal peptide. Compared with wild type (WT), the growth rate of transformants increased by 7.4%-18.5%, and the eicosapentaenoic acid content in an optimal transformant increased by 21.0%. Correspondingly, the intracellular ROS levels decreased by 56.9%-70.0%, and the catalase content in transformants was about 1.8 times that of WT. The photorespiration level of transformants was reduced by the measurement and calculation of the dissolved oxygen concentration under the condition of light-dark transition. The expression level of the key genes related to the photorespiration pathway in transformants was more than 80% lower than that in WT. These results indicated that Vitreoscilla hemoglobin could improve microalgal growth by reducing ROS damage and modulating photorespiration under stress conditions.
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Affiliation(s)
- Xiao-Ting Ding
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Yong Fan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Er-Ying Jiang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Yi Shi
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | | | - Guang-Rong Hu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Fu-Li Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao 266101, China,; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China.
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Cui Y, Wang K, Xu W, Wang Y, Gao Z, Cui H, Meng C, Qin S. Plastid Engineering of a Marine Alga, Nannochloropsis gaditana, for Co-Expression of Two Recombinant Peptides. JOURNAL OF PHYCOLOGY 2021; 57:569-576. [PMID: 33174215 DOI: 10.1111/jpy.13099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/16/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
The purpose of this study was to establish a plastid transformation system for expressing recombinant proteins in Nannochloropsis gaditana. On the basis of the sequenced plastid genome, the homologous flanking region, 16S-trnI/trnA-23S, and the endogenous regulatory fragments containing the psbA promoter, rbcL promoter, rbcL terminator, and psbA terminator were amplified from N. gaditana as elements of a plastid transformation vector. Then, the herbicide-resistant gene (bar) was used as a selectable marker, regulated by the psbA promoter and rbcL terminator. Finally, two codon-optimized antimicrobial peptide-coding genes linked by endogenous ribosome binding site (RBS) in a polycistron were inserted into the constructed vector under the regulation of the rbcL promoter and psbA terminator. After microparticle bombardment, the positive clones were detected using polymerase chain reaction (PCR), and Southern and Western blotting were used to assess the co-expression of the two antimicrobial peptides from the plastid. Nannochloropsis gaditana showed the potential to express recombinant proteins for biotechnological applications, for example, for the development of oral vaccines in aquaculture.
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Affiliation(s)
- Yulin Cui
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Kang Wang
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, China
| | - Wenxin Xu
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, 030801, China
| | - Yinchu Wang
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Zhengquan Gao
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, China
| | - Hongli Cui
- Institute of Molecular Agriculture and Bioenergy, Shanxi Agricultural University, Taigu, 030801, China
| | - Chunxiao Meng
- School of Life Sciences, Shandong University of Technology, Zibo, 255049, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
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5
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Environmental palaeogenomic reconstruction of an Ice Age algal population. Commun Biol 2021; 4:220. [PMID: 33594237 PMCID: PMC7887274 DOI: 10.1038/s42003-021-01710-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA. Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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6
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Cecchin M, Berteotti S, Paltrinieri S, Vigliante I, Iadarola B, Giovannone B, Maffei ME, Delledonne M, Ballottari M. Improved lipid productivity in Nannochloropsis gaditana in nitrogen-replete conditions by selection of pale green mutants. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:78. [PMID: 32336989 PMCID: PMC7175523 DOI: 10.1186/s13068-020-01718-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Nannochloropsis gaditana is a photosynthetic unicellular microalgae considered one of the most interesting marine algae to produce biofuels and food additive due to its rapid growth rate and high lipid accumulation. Although microalgae are attractive platforms for solar energy bioconversion, the overall efficiency of photosynthesis is reduced due to the steep light gradient in photobioreactors. Moreover, accumulation of lipids in microalgae for biofuels production is usually induced in a two-phase cultivation process by nutrient starvation, with additional time and costs associated. In this work, a biotechnological approach was directed for the isolation of strains with improved light penetration in photobioreactor combined with increased lipids productivity. RESULTS Mutants of Nannochloropsis gaditana were obtained by chemical mutagenesis and screened for having both a reduced chlorophyll content per cell and increased affinity for Nile red, a fluorescent dye which binds to cellular lipid fraction. Accordingly, one mutant, called e8, was selected and characterized for having a 30% reduction of chlorophyll content per cell and an almost 80% increase of lipid productivity compared to WT in nutrient-replete conditions, with C16:0 and C18:0 fatty acids being more than doubled in the mutant. Whole-genome sequencing revealed mutations in 234 genes in e8 mutant among which there is a non-conservative mutation in the dgd1 synthase gene. This gene encodes for an enzyme involved in the biosynthesis of DGDG, one of the major lipids found in the thylakoid membrane and it is thus involved in chloroplast biogenesis. Lipid biosynthesis is strongly influenced by light availability in several microalgae species, including Nannochloropsis gaditana: reduced chlorophyll content per cell and more homogenous irradiance in photobioreactor is at the base for the increased lipid productivity observed in the e8 mutant. CONCLUSIONS The results herein obtained presents a promising strategy to produce algal biomass enriched in lipid fraction to be used for biofuel and biodiesel production in a single cultivation process, without the additional complexity of the nutrient starvation phase. Genome sequencing and identification of the mutations introduced in e8 mutant suggest possible genes responsible for the observed phenotypes, identifying putative target for future complementation and biotechnological application.
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Affiliation(s)
- Michela Cecchin
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Silvia Berteotti
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Stefania Paltrinieri
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Ivano Vigliante
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Unità di Fisiologia Vegetale, Università di Torino, Via Quarello 15/a, 10135 Turin, Italy
| | - Barbara Iadarola
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Barbara Giovannone
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Massimo E. Maffei
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Unità di Fisiologia Vegetale, Università di Torino, Via Quarello 15/a, 10135 Turin, Italy
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
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Saldarriaga LF, Almenglo F, Ramírez M, Cantero D. Kinetic characterization and modeling of a microalgae consortium isolated from landfill leachate under a high CO2 concentration in a bubble column photobioreactor. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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8
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Pandeirada CO, Maricato É, Ferreira SS, Correia VG, Pinheiro BA, Evtuguin DV, Palma AS, Correia A, Vilanova M, Coimbra MA, Nunes C. Structural analysis and potential immunostimulatory activity of Nannochloropsis oculata polysaccharides. Carbohydr Polym 2019; 222:114962. [DOI: 10.1016/j.carbpol.2019.06.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/17/2019] [Accepted: 06/03/2019] [Indexed: 11/27/2022]
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9
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High efficiency transformation by electroporation of the freshwater alga Nannochloropsis limnetica. World J Microbiol Biotechnol 2019; 35:119. [DOI: 10.1007/s11274-019-2695-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/12/2019] [Indexed: 10/26/2022]
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10
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Guo L, Liang S, Zhang Z, Liu H, Wang S, Pan K, Xu J, Ren X, Pei S, Yang G. Genome assembly of Nannochloropsis oceanica provides evidence of host nucleus overthrow by the symbiont nucleus during speciation. Commun Biol 2019; 2:249. [PMID: 31286066 PMCID: PMC6610115 DOI: 10.1038/s42003-019-0500-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/29/2019] [Indexed: 11/08/2022] Open
Abstract
The species of the genus Nannochloropsis are unique in their maintenance of a nucleus-plastid continuum throughout their cell cycle, non-motility and asexual reproduction. These characteristics should have been endorsed in their gene assemblages (genomes). Here we show that N. oceanica has a genome of 29.3 Mb consisting of 32 pseudochromosomes and containing 7,330 protein-coding genes; and the host nucleus may have been overthrown by an ancient red alga symbiont nucleus during speciation through secondary endosymbiosis. In addition, N. oceanica has lost its flagella and abilities to undergo meiosis and sexual reproduction, and adopted a genome reduction strategy during speciation. We propose that N. oceanica emerged through the active fusion of a host protist and a photosynthesizing ancient red alga and the symbiont nucleus became dominant over the host nucleus while the chloroplast was wrapped by two layers of endoplasmic reticulum. Our findings evidenced an alternative speciation pathway of eukaryotes.
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Affiliation(s)
- Li Guo
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
| | - Sijie Liang
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
| | - Zhongyi Zhang
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
| | - Hang Liu
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
| | - Songwen Wang
- College of Agriculture and Resources and Environment, Tianjin Agricultural University, Tianjin, 300384 P. R. China
| | - Kehou Pan
- Laboratory of Applied Microalgae, College of Fisheries, OUC, Qingdao, 266003 P. R. China
| | - Jian Xu
- Functional Genomics Group, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 P. R. China
| | - Xue Ren
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, 100176 P. R. China
| | - Surui Pei
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing, 100176 P. R. China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China (OUC), Qingdao, 266003 P. R. China
- Institutes of Evolution and Marine Biodiversity, OUC, Qingdao, 266003 P. R. China
- Key Laboratory of Marine Genetics and Breeding of Ministry of Education, OUC, Qingdao, 266003 P. R. China
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11
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Stoykova P, Stoyneva-Gärtner M, Uzunov B, Gärtner G, Atanassov I, Draganova P, Borisova C. Morphological characterization and phylogenetic analysis of aeroterrestrial Vischeria/Eustigmatos strains with industrial potential. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2018.1561212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Petya Stoykova
- Plant Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Maya Stoyneva-Gärtner
- Department of Botany, Faculty of Biology, Sofia University “St Kliment Ohridski”, Sofia, Bulgaria
| | - Blagoy Uzunov
- Department of Botany, Faculty of Biology, Sofia University “St Kliment Ohridski”, Sofia, Bulgaria
| | - Georg Gärtner
- Institut für Botanik, Fakultät für Biologie, Üniversitat Innsbruck, Austria
| | - Ivan Atanassov
- Plant Genetics Group, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Petya Draganova
- Department of Botany, Faculty of Biology, Sofia University “St Kliment Ohridski”, Sofia, Bulgaria
| | - Cvetanka Borisova
- Department of Botany, Faculty of Biology, Sofia University “St Kliment Ohridski”, Sofia, Bulgaria
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12
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Poliner E, Farré EM, Benning C. Advanced genetic tools enable synthetic biology in the oleaginous microalgae Nannochloropsis sp. PLANT CELL REPORTS 2018; 37:1383-1399. [PMID: 29511798 DOI: 10.1007/s00299-018-2270-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/26/2018] [Indexed: 05/16/2023]
Abstract
Nannochloropsis is a genus of fast-growing microalgae that are regularly used for biotechnology applications. Nannochloropsis species have a high triacylglycerol content and their polar lipids are rich in the omega-3 long-chain polyunsaturated fatty acid, eicosapentaenoic acid. Placed in the heterokont lineage, the Nannochloropsis genus has a complex evolutionary history. Genome sequences are available for several species, and a number of transcriptomic datasets have been produced, making this genus a facile model for comparative genomics. There is a growing interest in Nannochloropsis species as models for the study of microalga lipid metabolism and as a chassis for synthetic biology. Recently, techniques for gene stacking, and targeted gene disruption and repression in the Nannochloropsis genus have been developed. These tools enable gene-specific, mechanistic studies and have already allowed the engineering of improved Nannochloropsis strains with superior growth, or greater bioproduction.
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Affiliation(s)
- Eric Poliner
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Christoph Benning
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
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13
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Soria-Verdugo A, Goos E, García-Hernando N, Riedel U. Analyzing the pyrolysis kinetics of several microalgae species by various differential and integral isoconversional kinetic methods and the Distributed Activation Energy Model. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Wei L, Xu J. Optimized methods of chromatin immunoprecipitation for profiling histone modifications in industrial microalgae Nannochloropsis spp. JOURNAL OF PHYCOLOGY 2018; 54:358-367. [PMID: 29444334 DOI: 10.1111/jpy.12623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/11/2018] [Indexed: 06/08/2023]
Abstract
Epigenetic factors such as histone modifications play integral roles in plant development and stress response, yet their implications in algae remain poorly understood. In the industrial oleaginous microalgae Nannochloropsis spp., the lack of an efficient methodology for chromatin immunoprecipitation (ChIP), which determines the specific genomic location of various histone modifications, has hindered probing the epigenetic basis of their photosynthetic carbon conversion and storage as oil. Here, a detailed ChIP protocol was developed for Nannochloropsis oceanica, which represents a reliable approach for the analysis of histone modifications, chromatin state, and transcription factor-binding sites at the epigenetic level. Using ChIP-qPCR, genes related to photosynthetic carbon fixation in this microalga were systematically assessed. Furthermore, a ChIP-Seq protocol was established and optimized, which generated a genome-wide profile of histone modification events, using histone mark H3K9Ac as an example. These results are the first step for appreciation of the chromatin landscape in industrial oleaginous microalgae and for epigenetics-based microalgal feedstock development.
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Affiliation(s)
- Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Safafar H, Hass MZ, Møller P, Holdt SL, Jacobsen C. High-EPA Biomass from Nannochloropsis salina Cultivated in a Flat-Panel Photo-Bioreactor on a Process Water-Enriched Growth Medium. Mar Drugs 2016; 14:md14080144. [PMID: 27483291 PMCID: PMC4999905 DOI: 10.3390/md14080144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/21/2016] [Accepted: 07/25/2016] [Indexed: 12/17/2022] Open
Abstract
Nannochloropsis salina was grown on a mixture of standard growth media and pre-gasified industrial process water representing effluent from a local biogas plant. The study aimed to investigate the effects of enriched growth media and cultivation time on nutritional composition of Nannochloropsis salina biomass, with a focus on eicosapentaenoic acid (EPA). Variations in fatty acid composition, lipids, protein, amino acids, tocopherols and pigments were studied and results compared to algae cultivated on F/2 media as reference. Mixed growth media and process water enhanced the nutritional quality of Nannochloropsis salina in laboratory scale when compared to algae cultivated in standard F/2 medium. Data from laboratory scale translated to the large scale using a 4000 L flat panel photo-bioreactor system. The algae growth rate in winter conditions in Denmark was slow, but results revealed that large-scale cultivation of Nannochloropsis salina at these conditions could improve the nutritional properties such as EPA, tocopherol, protein and carotenoids compared to laboratory-scale cultivated microalgae. EPA reached 44.2% ± 2.30% of total fatty acids, and α-tocopherol reached 431 ± 28 µg/g of biomass dry weight after 21 days of cultivation. Variations in chemical compositions of Nannochloropsis salina were studied during the course of cultivation. Nannochloropsis salina can be presented as a good candidate for winter time cultivation in Denmark. The resulting biomass is a rich source of EPA and also a good source of protein (amino acids), tocopherols and carotenoids for potential use in aquaculture feed industry.
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Affiliation(s)
- Hamed Safafar
- Technical University of Denmark, National Food Institute (DTU Food), Søltofts Plads, Building 221, Kongens Lyngby 2800, Denmark.
| | - Michael Z Hass
- Kalundborg Municipality, Department Development, Torvet 3A, Kalundborg 4400, Denmark.
| | - Per Møller
- Kalundborg Municipality, Department Development, Torvet 3A, Kalundborg 4400, Denmark.
| | - Susan L Holdt
- Technical University of Denmark, National Food Institute (DTU Food), Søltofts Plads, Building 221, Kongens Lyngby 2800, Denmark.
| | - Charlotte Jacobsen
- Technical University of Denmark, National Food Institute (DTU Food), Søltofts Plads, Building 221, Kongens Lyngby 2800, Denmark.
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Zepeda Mendoza ML, Lundberg J, Ivarsson M, Campos P, Nylander JAA, Sallstedt T, Dalen L. Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden. PLoS One 2016; 11:e0151577. [PMID: 26985997 PMCID: PMC4795671 DOI: 10.1371/journal.pone.0151577] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 03/01/2016] [Indexed: 02/01/2023] Open
Abstract
Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante's cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante's cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem's different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.
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Affiliation(s)
| | - Johannes Lundberg
- Department of Botany, Swedish Museum of Natural History, Stockholm, Sweden
| | - Magnus Ivarsson
- Department of Palaeobiology and the Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, Stockholm, Sweden
| | - Paula Campos
- Centre for GeoGenetics, University of Copenhagen, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Johan A. A. Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Therese Sallstedt
- Department of Palaeobiology and the Nordic Center for Earth Evolution (NordCEE), Swedish Museum of Natural History, Stockholm, Sweden
| | - Love Dalen
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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17
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Abstract
Plant and algal oils are some of the most energy-dense renewable compounds provided by nature. Triacylglycerols (TAGs) are the major constituent of plant oils, which can be converted into fatty acid methyl esters commonly known as biodiesel. As one of the most efficient producers of TAGs, photosynthetic microalgae have attracted substantial interest for renewable fuel production. Currently, the big challenge of microalgae based TAGs for biofuels is their high cost compared to fossil fuels. A conundrum is that microalgae accumulate large amounts of TAGs only during stress conditions such as nutrient deprivation and temperature stress, which inevitably will inhibit growth. Thus, a better understanding of why and how microalgae induce TAG biosynthesis under stress conditions would allow the development of engineered microalgae with increased TAG production during conditions optimal for growth. Land plants also synthesize TAGs during stresses and we will compare new findings on environmental stress-induced TAG accumulation in plants and microalgae especially in the well-characterized model alga Chlamydomonas reinhardtii and a biotechnologically relevant genus Nannochloropsis.
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Affiliation(s)
- Zhi-Yan Du
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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18
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Zhang X, Kan J, Wang J, Gu H, Hu J, Zhao Y, Sun J. First record of a large-scale bloom-causing species Nannochloropsis granulata (Monodopsidaceae, Eustigmatophyceae) in China Sea waters. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:1430-1441. [PMID: 26024617 DOI: 10.1007/s10646-015-1466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/28/2015] [Indexed: 06/04/2023]
Abstract
Nannochloropsis is an ubiquitous genus, found in diverse aquatic environments including open ocean as well as fresh and brackish water. Recently, large-scale blooms occurred frequently along eutrophic coastal zone from the Bohai Sea to the northern Yellow Sea in China. The cell density reached 10(9) to 10(10)cells per liter during a bloom near Qinhuangdao, Hebei Province. The bloom forming species, a yellow-green microalgae was successfully isolated and cultivated in the laboratory. Microscopic observation indicated that the cells contained simple morphological characteristics with a diameter about 2 μm. Pigment analyses confirmed that the pigment composition of the newly isolated strain BDH02 was similar to that of Nannochloropsis granulata. Phylogenetic analyses of 18S rRNA gene, ITS, and rbcL gene indicated that the strain was closely related to N. granulata. This is the first record of a bloom caused by N. granulata in China.
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Affiliation(s)
- Xiaodong Zhang
- College of Marine Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, China
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin, 300457, People's Republic of China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, PA, 19311, USA
| | - Jing Wang
- College of Marine Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, China
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin, 300457, People's Republic of China
| | - Haifeng Gu
- Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, China
| | - Jun Hu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
| | - Yuan Zhao
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jun Sun
- College of Marine Science and Engineering, Tianjin University of Science and Technology, Tianjin, 300457, China.
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19
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Kaye Y, Grundman O, Leu S, Zarka A, Zorin B, Didi-Cohen S, Khozin-Goldberg I, Boussiba S. Metabolic engineering toward enhanced LC-PUFA biosynthesis in Nannochloropsis oceanica : Overexpression of endogenous Δ12 desaturase driven by stress-inducible promoter leads to enhanced deposition of polyunsaturated fatty acids in TAG. ALGAL RES 2015. [DOI: 10.1016/j.algal.2015.05.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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20
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Taleb A, Pruvost J, Legrand J, Marec H, Le-Gouic B, Mirabella B, Legeret B, Bouvet S, Peltier G, Li-Beisson Y, Taha S, Takache H. Development and validation of a screening procedure of microalgae for biodiesel production: application to the genus of marine microalgae Nannochloropsis. BIORESOURCE TECHNOLOGY 2015; 177:224-32. [PMID: 25496942 DOI: 10.1016/j.biortech.2014.11.068] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 11/14/2014] [Accepted: 11/15/2014] [Indexed: 05/21/2023]
Abstract
Nannochloropsis has emerged as a promising alga for biodiesel production. However, the genus consists of 6 species and hundreds of strains making strain selection a challenge. Furthermore, oil productivity is instrumental to economic viability of any algal strain for industrial production, which is dependent on growth rate and oil content. In most cases, these two parameters have been studied independently. Thus, the goal of this study is to provide a combined method for evaluating strain performance in specially designed photobioreactors together with an in-depth lipidomic analyses. The nine strains of Nannochloropsis tested showed considerable variations in productivity and lipidomics highlighting the importance of strain selection. Finally, Nannochloropsis gaditana CCMP527 and Nannochloropsis salina CCMP537 emerged as the two most promising strains, with an oil content of 37 and 27 dry wt% after 11-day nitrogen starvation, respectively, resulting in TAG productivity of 13×10(-3) and 18×10(-3) kg m(-3) d(-1), respectively.
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Affiliation(s)
- A Taleb
- GEPEA, Université de Nantes, CNRS, UMR6144, bd de l'Université, CRTT, BP 406, 44602 Saint-Nazaire Cedex, France; Department of Food Science and Technology, Faculty of Agricultural and Veterinary Medicine, Lebanese University, Dekwaneh, Beirut, Lebanon; AZM Center for Biotechnology Research and its Applications, Laboratory of Applied Biotechnology, Lebanese University, EDST, Tripoli, Lebanon
| | - J Pruvost
- GEPEA, Université de Nantes, CNRS, UMR6144, bd de l'Université, CRTT, BP 406, 44602 Saint-Nazaire Cedex, France.
| | - J Legrand
- GEPEA, Université de Nantes, CNRS, UMR6144, bd de l'Université, CRTT, BP 406, 44602 Saint-Nazaire Cedex, France
| | - H Marec
- GEPEA, Université de Nantes, CNRS, UMR6144, bd de l'Université, CRTT, BP 406, 44602 Saint-Nazaire Cedex, France
| | - B Le-Gouic
- GEPEA, Université de Nantes, CNRS, UMR6144, bd de l'Université, CRTT, BP 406, 44602 Saint-Nazaire Cedex, France
| | - B Mirabella
- CEA, IBEB, Lab Bioenerget Biotechnol Bacteries & Microalgues, Saint-Paul-lez-Durance, F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France; Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - B Legeret
- CEA, IBEB, Lab Bioenerget Biotechnol Bacteries & Microalgues, Saint-Paul-lez-Durance, F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France; Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - S Bouvet
- CEA, IBEB, Lab Bioenerget Biotechnol Bacteries & Microalgues, Saint-Paul-lez-Durance, F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France; Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - G Peltier
- CEA, IBEB, Lab Bioenerget Biotechnol Bacteries & Microalgues, Saint-Paul-lez-Durance, F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France; Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - Y Li-Beisson
- CEA, IBEB, Lab Bioenerget Biotechnol Bacteries & Microalgues, Saint-Paul-lez-Durance, F-13108, France; CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, F-13108, France; Aix Marseille Université, BVME UMR7265, Marseille, F-13284, France
| | - S Taha
- Department of Food Science and Technology, Faculty of Agricultural and Veterinary Medicine, Lebanese University, Dekwaneh, Beirut, Lebanon
| | - H Takache
- AZM Center for Biotechnology Research and its Applications, Laboratory of Applied Biotechnology, Lebanese University, EDST, Tripoli, Lebanon
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21
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Ultrastructure and composition of the Nannochloropsis gaditana cell wall. EUKARYOTIC CELL 2014; 13:1450-64. [PMID: 25239976 DOI: 10.1128/ec.00183-14] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Marine algae of the genus Nannochloropsis are promising producers of biofuel precursors and nutraceuticals and are also harvested commercially for aquaculture feed. We have used quick-freeze, deep-etch electron microscopy, Fourier transform infrared spectroscopy, and carbohydrate analyses to characterize the architecture of the Nannochloropsis gaditana (strain CCMP 526) cell wall, whose recalcitrance presents a significant barrier to biocommodity extraction. The data indicate a bilayer structure consisting of a cellulosic inner wall (~75% of the mass balance) protected by an outer hydrophobic algaenan layer. Cellulase treatment of walls purified after cell lysis generates highly enriched algaenan preparations without using the harsh chemical treatments typically used in algaenan isolation and characterization. Nannochloropsis algaenan was determined to comprise long, straight-chain, saturated aliphatics with ether cross-links, which closely resembles the cutan of vascular plants. Chemical identification of >85% of the isolated cell wall mass is detailed, and genome analysis is used to identify candidate biosynthetic enzymes.
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22
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Li F, Gao D, Hu H. High-efficiency nuclear transformation of the oleaginous marine Nannochloropsis species using PCR product. Biosci Biotechnol Biochem 2014; 78:812-7. [DOI: 10.1080/09168451.2014.905184] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Nannochloropsis are model species for investigating biofuel production by algae. To develop them into an integrated photons-to-fuel production platform, high efficiency transformation methods are necessary. Here, we obtained the β-tubulin promoter regions of all recognized species of genus Nannochloropsis, and successfully transformed all five marine species by electroporation. In addition, the PCR amplified double stranded DNA fragments (PCR fragments) based transformation system was established in these Nannochloropsis species, which showed much higher transformation efficiency (10.7–61.2 × 10−6, 1.5–13-fold) than that of linearized plasmid based transformation. The cotransformation of N. salina using a circular plasmid containing a non-selectable GUS gene and a PCR fragment containing only a selection marker cassette was also achieved and found to be very efficient (over 50%). This simple and highly efficient transformation protocol reported in our study provided a useful tool for gene functional analysis and genetic engineering of the oleaginous Nannochloropsis species.
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Affiliation(s)
- Fengjuan Li
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Dawen Gao
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, China
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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23
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Starkenburg SR, Kwon KJ, Jha RK, McKay C, Jacobs M, Chertkov O, Twary S, Rocap G, Cattolico RA. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics 2014; 15:212. [PMID: 24646409 PMCID: PMC3999925 DOI: 10.1186/1471-2164-15-212] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 03/11/2014] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776. RESULTS The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome). CONCLUSIONS Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.
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Affiliation(s)
- Shawn R Starkenburg
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Kyungyoon J Kwon
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley 94720, CA, USA
| | - Ramesh K Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Cedar McKay
- School of Oceanography, University of Washington, Seattle 98195, WA, USA
| | - Michael Jacobs
- Biology Department, University of Washington, Seattle 98195, WA, USA
| | - Olga Chertkov
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Scott Twary
- Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA
| | - Gabrielle Rocap
- School of Oceanography, University of Washington, Seattle 98195, WA, USA
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24
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Pal D, Khozin-Goldberg I, Didi-Cohen S, Solovchenko A, Batushansky A, Kaye Y, Sikron N, Samani T, Fait A, Boussiba S. Growth, lipid production and metabolic adjustments in the euryhaline eustigmatophyte Nannochloropsis oceanica CCALA 804 in response to osmotic downshift. Appl Microbiol Biotechnol 2013; 97:8291-306. [DOI: 10.1007/s00253-013-5092-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 12/24/2022]
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25
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Zhu Y, Dunford NT. Growth and Biomass Characteristics of Picochlorum oklahomensis and Nannochloropsis oculata. J AM OIL CHEM SOC 2013. [DOI: 10.1007/s11746-013-2225-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Genet 2012; 8:e1003064. [PMID: 23166516 PMCID: PMC3499364 DOI: 10.1371/journal.pgen.1003064] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 08/29/2012] [Indexed: 11/18/2022] Open
Abstract
Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogen-depleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica-specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis species by a growing academic community focused on this genus.
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27
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Pan K, Qin J, Li S, Dai W, Zhu B, Jin Y, Yu W, Yang G, Li D. NUCLEAR MONOPLOIDY AND ASEXUAL PROPAGATION OF NANNOCHLOROPSIS OCEANICA (EUSTIGMATOPHYCEAE) AS REVEALED BY ITS GENOME SEQUENCE(1). JOURNAL OF PHYCOLOGY 2011; 47:1425-1432. [PMID: 27020366 DOI: 10.1111/j.1529-8817.2011.01057.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Species in genus Nannochloropsis are promising candidates for both biofuel and biomass production due to their ability to accumulate rich fatty acids and grow fast; however, their sexual reproduction has not been studied. It is clear that the construction of their metabolic pathways, such as that of polyunsaturated fatty acid (PUFA) biosynthesis, and understanding of their biological characteristics, such as nuclear ploidy and reproductive strategy, will certainly facilitate their genetic improvement through gene engineering and mutation and clonal expansion. In this study, the genome of N. oceanica S. Suda et Miyashita was sequenced with the next-generation Illumina GA sequencing technologies. The genome was ∼30 Mb in size, which contained 11,129 protein-encoding genes. Of them, 59.65% were annotated by aligning with those in diverse protein databases, and 29.68% were assigned at least one function described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Less frequent polymorphic nucleotides (one in 22.06 kb) and the obvious deviation from 1:1 (major:minor, minor ≥10) expectation indicated the nuclear monoploidy of N. oceanica. The lack of the majority of meiosis-specific proteins implied the asexual reproduction of this alga. In combination, the nuclear monoploidy and asexual propagation led us to favor the hypothesis that N. oceanica was a premeiotic or ameiotic alga. In addition, sequence similarity-based searching identified the elongase- and desaturase-encoding genes involved in the biosynthesis of long-chain PUFAs, which provided the genetic basis of its rich content of eicosapentaenoic acid (EPA). The functional genes and their metabolic pathways profiled against its genome sequence will facilitate its integrative investigations.
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Affiliation(s)
- Kehou Pan
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Junjie Qin
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Si Li
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Wenkui Dai
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Baohua Zhu
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Yuanchun Jin
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Wengong Yu
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Guanpin Yang
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Dongfang Li
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
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High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp. Proc Natl Acad Sci U S A 2011; 108:21265-9. [PMID: 22123974 DOI: 10.1073/pnas.1105861108] [Citation(s) in RCA: 340] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Algae have reemerged as potential next-generation feedstocks for biofuels, but strain improvement and progress in algal biology research have been limited by the lack of advanced molecular tools for most eukaryotic microalgae. Here we describe the development of an efficient transformation method for Nannochloropsis sp., a fast-growing, unicellular alga capable of accumulating large amounts of oil. Moreover, we provide additional evidence that Nannochloropsis is haploid, and we demonstrate that insertion of transformation constructs into the nuclear genome can occur by high-efficiency homologous recombination. As examples, we generated knockouts of the genes encoding nitrate reductase and nitrite reductase, resulting in strains that were unable to grow on nitrate and nitrate/nitrite, respectively. The application of homologous recombination in this industrially relevant alga has the potential to rapidly advance algal functional genomics and biotechnology.
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Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol 2009; 75:5797-808. [PMID: 19592529 DOI: 10.1128/aem.00298-09] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.
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Vaulot D, Eikrem W, Viprey M, Moreau H. The diversity of small eukaryotic phytoplankton (≤3 μm) in marine ecosystems. FEMS Microbiol Rev 2008; 32:795-820. [DOI: 10.1111/j.1574-6976.2008.00121.x] [Citation(s) in RCA: 304] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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31
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Fawley KP, Fawley MW. Observations on the Diversity and Ecology of Freshwater Nannochloropsis (Eustigmatophyceae), with Descriptions of New Taxa. Protist 2007; 158:325-36. [PMID: 17576099 DOI: 10.1016/j.protis.2007.03.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Accepted: 03/31/2007] [Indexed: 11/23/2022]
Abstract
The genus Nannochloropsis is well known from the marine environment but has only recently been reported from fresh and brackish waters. A single species, N. limnetica, was first documented from shallow lakes in Germany, where it produced spring blooms. A second unnamed isolate from a river in the United States has been characterized by sequence analysis and light microscopy. All of the Nannochloropsis species that have been described, both marine and freshwater, are small spheres with essentially no distinguishing morphological characteristics. Therefore, they must be characterized using molecular techniques. We have cultured numerous isolates of Nannochloropsis from a series of lakes on the James River in the Arrowwood National Wildlife Refuge, North Dakota, USA, and 1 isolate from a pond in Itasca State Park, Minnesota, USA. The diversity among these isolates was determined by light microscopy and DNA sequence analysis. Seven distinct haplotypes of Nannochloropsis were found, one of which possesses 18S rDNA and rbcL sequences identical to those of N. limnetica from Europe. The 6 new haplotypes vary in rbcL sequences and some are morophologically distinct from each other and from N. limnetica. These types are described as the new taxa N. limnetica var. globosa, N. limnetica var. irregularis, N. limnetica var. dystrophica, and N. limnetica var. gutta. All of the Nannochloropsis isolates from Arrowwood and Itasca were cultured only from samples taken during cold-water periods. These results suggest that Nannochloropsis species may be better adapted to cold water conditions, including temperatures near 0 degrees C and ice cover.
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MESH Headings
- Algal Proteins/genetics
- Cold Temperature
- DNA, Algal/chemistry
- DNA, Algal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Eukaryota/classification
- Eukaryota/cytology
- Eukaryota/genetics
- Eukaryota/isolation & purification
- Fresh Water/parasitology
- Genes, rRNA
- Haplotypes
- Minnesota
- Molecular Sequence Data
- North Dakota
- Phylogeny
- RNA, Algal/genetics
- RNA, Ribosomal, 18S/genetics
- Ribulose-Bisphosphate Carboxylase/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Karen P Fawley
- School of Mathematical and Natural Sciences, University of Arkansas at Monticello, Monticello, AR 71656, USA.
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32
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Negrisolo E, Maistro S, Incarbone M, Moro I, Dalla Valle L, Broady PA, Andreoli C. Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes. Mol Phylogenet Evol 2004; 33:156-70. [PMID: 15324845 DOI: 10.1016/j.ympev.2004.04.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2003] [Revised: 04/01/2004] [Indexed: 11/26/2022]
Abstract
Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.
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Affiliation(s)
- Enrico Negrisolo
- Department of Biology and Centro Ricerche Interdipartimentale Biotecnologie Innovative (CRIBI), University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy
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Andersen RA. Biology and systematics of heterokont and haptophyte algae. AMERICAN JOURNAL OF BOTANY 2004; 91:1508-1522. [PMID: 21652306 DOI: 10.3732/ajb.91.10.1508] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this paper, I review what is currently known of phylogenetic relationships of heterokont and haptophyte algae. Heterokont algae are a monophyletic group that is classified into 17 classes and represents a diverse group of marine, freshwater, and terrestrial algae. Classes are distinguished by morphology, chloroplast pigments, ultrastructural features, and gene sequence data. Electron microscopy and molecular biology have contributed significantly to our understanding of their evolutionary relationships, but even today class relationships are poorly understood. Haptophyte algae are a second monophyletic group that consists of two classes of predominately marine phytoplankton. The closest relatives of the haptophytes are currently unknown, but recent evidence indicates they may be part of a large assemblage (chromalveolates) that includes heterokont algae and other stramenopiles, alveolates, and cryptophytes. Heterokont and haptophyte algae are important primary producers in aquatic habitats, and they are probably the primary carbon source for petroleum products (crude oil, natural gas).
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Affiliation(s)
- Robert A Andersen
- Bigelow Laboratory for Ocean Sciences, P.O. Box 475, West Boothbay Harbor, Maine 04575 USA
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Ben Ali A, De Baere R, De Wachter R, Van de Peer Y. Evolutionary relationships among heterokont algae (the autotrophic stramenopiles) based on combined analyses of small and large subunit ribosomal RNA. Protist 2002; 153:123-32. [PMID: 12125754 DOI: 10.1078/1434-4610-00091] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to study the phylogenetic relationships within the stramenopiles, and particularly among the heterokont algae, we have determined complete or nearly complete large-subunit ribosomal RNA sequences for different species of raphidophytes, phaeophytes, xanthophytes, chrysophytes, synurophytes and pinguiophytes. With the small- and large-subunit ribosomal RNA sequences of representatives for nearly all known groups of heterokont algae, phylogenetic trees were constructed from a concatenated alignment of both ribosomal RNAs, including more than 5,000 positions. By using different tree construction methods, inferred phylogenies showed phaeophytes and xanthophytes as sister taxa, as well as the pelagophytes and dictyochophytes, and the chrysophytes/synurophytes and eustigmatophytes. All these relationships are highly supported by bootstrap analysis. However, apart from these sister group relationships, very few other internodes are well resolved and most groups of heterokont algae seem to have diverged within a relatively short time frame.
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Blomster J, Hoey EM, Maggs CA, Stanhope MJ. Species-specific oligonucleotide probes for macroalgae: molecular discrimination of two marine fouling species of Enteromorpha (Ulvophyceae). Mol Ecol 2000; 9:177-86. [PMID: 10672161 DOI: 10.1046/j.1365-294x.2000.00850.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The green seaweeds Enteromorpha intestinalis and E. compressa are important fouling organisms commonly found in polluted and nutrient-enriched marine and brackish water habitats, where they are used in environmental monitoring. Discrimination of the two species is extremely difficult because of overlapping morphological characters. In this study a quick molecular method for species identification was developed based on the nuclear rDNA ITS2 sequence data of 54 E. intestinalis samples and 20 E. compressa samples from a wide geographical range. Oligonucleotide probes were designed for species-specific hybridization to dot-blots of the PCR-amplified ITS1, 5.8S gene and ITS2 fragment of both E. intestinalis and E. compressa. Specificity of the oligonucleotide probes was confirmed by tests with taxonomically diverse species that could morphologically be confused with E. intestinalis or E. compressa. This is the first use of species-specific probes for macroalgae. The restriction endonuclease NruI digested specifically the amplified PCR product from E. compressa into two fragments detectable on agarose gels, but no suitable restriction sites were identifiable in the PCR product of E. intestinalis.
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Affiliation(s)
- J Blomster
- School of Biology and Biochemistry, Queen's University of Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, Northern Ireland, UK
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36
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Guillou L, Chrétiennot-Dinet MJ, Boulben S, Moon-van der Staay SY, Vaulot D. Symbiomonas scintillans gen. et sp. nov. and Picophagus flagellatus gen. et sp. nov. (Heterokonta): two new heterotrophic flagellates of picoplanktonic size. Protist 1999; 150:383-98. [PMID: 10714773 DOI: 10.1016/s1434-4610(99)70040-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Two new oceanic free-living heterotrophic Heterokonta species with picoplanktonic size (< 2 microm) are described. Symbiomonas scintillans Guillou et Chrétiennot-Dinet gen. et sp. nov. was isolated from samples collected both in the equatorial Pacific Ocean and the Mediterranean Sea. This new species possesses ultrastructural features of the bicosoecids, such as the absence of a helix in the flagellar transitional region (found in Cafeteria roenbergensis and in a few bicosoecids), and a flagellar root system very similar to that of C. roenbergensis, Acronema sippewissettensis, and Bicosoeca maris. This new species is characterized by a single flagellum with mastigonemes, the presence of endosymbiotic bacteria located close to the nucleus, the absence of a lorica and a R3 root composed of a 6+3+x microtubular structure. Phylogenetical analyses of nuclear-encoded SSU rDNA gene sequences indicate that this species is close to the bicosoecids C. roenbergensis and Siluania monomastiga. Picophagus flagellatus Guillou et Chrétiennot-Dinet gen. et sp. nov. was collected in the equatorial Pacific Ocean. Cells are naked and possess two flagella. This species is characterized by the lack of a transitional helix and lateral filaments on the flagellar tubular hairs, the absence of siliceous scales, two unequal flagella, R1 + R3 roots, and the absence of a rhizoplast. SSU rDNA analyses place this strain at the base of the Chrysophyceae/Synurophyceae lineages.
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Affiliation(s)
- L Guillou
- Station Biologique, CNRS, INSU et Université Pierre et Marie Curie, Roscoff, France.
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Guillou L, Moon-Van Der Staay SY, Claustre H, Partensky F, Vaulot D. Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions. Appl Environ Microbiol 1999; 65:4528-36. [PMID: 10508085 PMCID: PMC91603 DOI: 10.1128/aem.65.10.4528-4536.1999] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity and abundance of the Bolidophyceae (Heterokonta), a newly described picoplanktonic algal class which is a sister group to the diatoms, was assessed in the equatorial Pacific Ocean and in the Mediterranean Sea by culture isolation, molecular biology techniques, and pigment analyses. Eight strains of Bolidophyceae were isolated in culture from different mesotrophic and oligotrophic areas. The corresponding small subunit (SSU) rRNA gene sequences allowed us to design two probes specific for the Bolidophyceae. These probes have been used in natural samples (i) to selectively amplify and detect Bolidophyceae sequences and (ii) to quantify the relative abundance of Bolidophyceae within the picoeukaryote community. Sequences available to date indicate that the class Bolidophyceae comprises at least three different clades, two corresponding to the previously described species Bolidomonas pacifica and Bolidomonas mediterranea and the third one corresponding to a subspecies of B. pacifica. Amplification of the SSU rRNA gene from natural samples with universal primers and hybridization using a Bolidomonas-specific probe followed by a eukaryote-specific probe allowed us to estimate the contribution of the Bolidophyceae to the eukaryotic DNA in both Pacific and Mediterranean waters to be lower than 1%. Similarly, high-performance liquid chromatography analyses of fucoxanthin, the major carotenoid present in Bolidophyceae, indicated that less than 4% of the total chlorophyll a in the picoplanktonic fraction in the equatorial Pacific was due to Bolidophyceae. Consequently, although strains of Bolidophyceae have been isolated from samples collected at several stations, this new class seems to have been a minor component of the natural picoeukaryotic populations in the ecosystems investigated, at least during the periods sampled.
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Affiliation(s)
- L Guillou
- Station Biologique de Roscoff, UPR CNRS 9042, INSU, and Université Pierre et Marie Curie, F-29682 Roscoff Cedex, France.
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38
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Andersen RA, Van de Peer Y, Potter D, Sexton JP, Kawachi M, LaJeunesse T. Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae. Protist 1999; 150:71-84. [PMID: 10724520 DOI: 10.1016/s1434-4610(99)70010-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The nucleotide sequence for the nuclear-encoded small subunit ribosomal RNA gene (SSU rRNA) was determined for 24 species of the Chrysophyceae sensu stricto. These sequences were aligned, using primary and secondary structure, with nine previously published sequences for the Chrysophyceae, 14 for the Synurophyceae, and five for the Eustigmatophyceae (outgroup). Data analyses were the substitution rate calibration distance method using neighbor-joining (TREECON), Kimura 2-parameter neighbor-joining method (PAUP) and the maximum parsimony method (PAUP, PHYLIP). Trees from the analyses were largely congruent, but bootstrap support was weak at many nodes. The analyses recovered clades of uniflagellate and biflagellate organisms associated with current higher level taxonomy (e.g., subclass, order). The genus Ochromonas was polyphyletic, and O. tuberculata in particular was distantly related to the other Ochromonas species in the analysis. The family Paraphysomonadaceae occupied a basal position in three of four analyses. The class Synurophyceae appeared to be embedded within the Chrysophyceae, but bootstrap support was weak (< 50%) in all analyses except the PHYLIP parsimony analysis (= 81%). It was considered premature to place the Synurophyceae back into the Chrysophyceae based upon the analysis of one gene, especially given the ultrastructural and pigment differences between the two groups, but the relationship of these two groups deserves further study.
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Affiliation(s)
- R A Andersen
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME 04575, USA.
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