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Kim YJ, Kim HJ, Lee TK, Kang D, Kim H, Cho S, Kim JH, Jung SW. Determining ecological interactions of key dinoflagellate species using an intensive metabarcoding approach in a semi-closed coastal ecosystem of South Korea. HARMFUL ALGAE 2024; 138:102698. [PMID: 39244233 DOI: 10.1016/j.hal.2024.102698] [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: 05/01/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 09/09/2024]
Abstract
Marine phytoplankton communities are pivotal in biogeochemical cycles and impact global climate change. However, the dynamics of the dinoflagellate community, its co-occurrence relationship with other eukaryotic plankton communities, and environmental factors remain poorly understood. In this study, we aimed to analyze the temporal changes in the eukaryotic plankton community using a 18S rDNA metabarcoding approach. We performed intensive monitoring for 439 days at intervals of three days during the period from November 2018 to June 2020 (n = 260) in Jangmok Bay Time-series Monitoring Site in South Korea. Among the 16,224 amplicon sequence variants (ASVs) obtained, dinoflagellates were the most abundant in the plankton community (38 % of total relative abundance). The dinoflagellate community was divided into 21 groups via cluster analysis, which showed an annually similar distribution of low-temperature periods. Additionally, we selected 11 taxa that had an occurrence mean exceeding 1 % of the total dinoflagellate abundance, accounting for 93 % of the total dinoflagellate community: namely Heterocapsa rotundata, Gymnodinium sp., Akashiwo sanguinea, Amoebophrya sp., Euduboscquella sp., Spiniferites ramosus, Dissodinium pseudolunula, Sinophysis sp., Karlodinium veneficum, and Katodinium glaucum. The key dinoflagellate species were well represented at temporally variable levels over an entire year. Heterocapsa rotundata was not significantly affected by water temperature, whereas its dynamics were largely influenced by strong predation pressure, competition, and/or the supplementation of food sources. The growth of A. sanguinea was associated with dissolved inorganic phosphorus concentrations, while Euduboscquella sp. showed a significant relationship with D. pseudolunula and K. glaucum, largely representing a positive association that implies possible parasitic mechanisms. This study demonstrated interactions between key dinoflagellate species and the environment, as well as parasites, predators, competitors, and feeders.
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Affiliation(s)
- Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 656-834, Republic of Korea; Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 656-834, Republic of Korea; Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea; Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| | - Donhyug Kang
- Marine Domain & Security Research Department, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea
| | - Hansoo Kim
- Marine Domain & Security Research Department, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea
| | - Sungho Cho
- Marine Domain & Security Research Department, Korea Institute of Ocean Science & Technology, Busan 49111, Republic of Korea
| | - Jin Ho Kim
- Department of Earth and Marine Science, College of Ocean Sciences, Jeju National University, Jeju 63243, Republic of Korea
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 656-834, Republic of Korea; Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea.
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Choi DH, Yang W, Kim YE, Park BS, Sung J, Choi J, Rho JR, Han YS, Lee Y. Variability in Paralytic Shellfish Toxin Profiles and Dinoflagellate Diversity in Mussels and Seawater Collected during Spring in Korean Coastal Seawater. Toxins (Basel) 2024; 16:338. [PMID: 39195748 PMCID: PMC11359905 DOI: 10.3390/toxins16080338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
Paralytic shellfish toxins (PSTs) are potent neurotoxins produced by certain microalgae, particularly dinoflagellates, and they can accumulate in shellfish in coastal seawater and thus pose significant health risks to humans. To explore the relationship between toxicity and PST profiles in seawater and mussels, the spatiotemporal variations in PST concentrations and profiles were investigated along the southern coast of Korea under peak PST levels during spring. Seawater and mussel samples were collected biweekly from multiple stations, and the toxin concentrations in the samples were measured. Moreover, the dinoflagellate community composition was analyzed using next-generation sequencing to identify potential PST-producing species. The PST concentrations and toxin profiles showed substantial spatiotemporal variability, with GTX1 and GTX4 representing the dominant toxins in both samples, and C1/2 tending to be higher in seawater. Alexandrium species were identified as the primary sources of PSTs. Environmental factors such as water temperature and salinity influenced PST production. This study demonstrates that variability in the amount and composition of PSTs is due to intricate ecological interactions. To mitigate shellfish poisoning, continuous monitoring must be conducted to gain a deeper understanding of these interactions.
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Affiliation(s)
- Dong Han Choi
- Ocean Climate Response and Ecosystem Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea; (D.H.C.); (W.Y.)
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Wonseok Yang
- Ocean Climate Response and Ecosystem Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea; (D.H.C.); (W.Y.)
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Young-Eun Kim
- Environmental Measurement & Analysis Center, National Institute of Environmental Research, Incheon 22689, Republic of Korea;
| | - Bum Soo Park
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; (B.S.P.); (J.S.)
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Republic of Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Jiyeon Sung
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; (B.S.P.); (J.S.)
| | - Jaeho Choi
- School of Earth and Environmental Sciences, Seoul National University, Seoul 08826, Republic of Korea;
- Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung-Rae Rho
- Department of Oceanography, Kunsan National University, Kunsan 54150, Republic of Korea;
| | | | - Yeonjung Lee
- Ocean Climate Response and Ecosystem Research Department, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea; (D.H.C.); (W.Y.)
- Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
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Abraham JS, Somasundaram S, Maurya S, Sood U, Lal R, Toteja R, Makhija S. Insights into freshwater ciliate diversity through high throughput DNA metabarcoding. FEMS MICROBES 2024; 5:xtae003. [PMID: 38450097 PMCID: PMC10917447 DOI: 10.1093/femsmc/xtae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/03/2024] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
The freshwater bodies of India are highly biodiverse but still understudied, especially concerning ciliates. Ciliates constitute a significant portion of eukaryotic diversity and play crucial roles in microbial loops, nutrient recycling, and ecosystem maintenance. The present study aimed to elucidate ciliate diversity in three freshwater sites in the Delhi region of India: Okhla Bird Sanctuary (OBS), Sanjay Lake (SL), and Raj Ghat pond (RJ). This study represents the first investigation into the taxonomic diversity and richness of freshwater ciliates in India using a high-throughput DNA metabarcoding approach. For the analysis, total environmental DNA was extracted from the three freshwater samples, followed by sequencing of the 18S V4 barcode region and subsequent phylogenetic analyses. Operational taxonomic units (OTU) analyses revealed maximum species diversity in OBS (106), followed by SL (104) and RJ (99) sites. Ciliates from the classes Oligohymenophorea, Prostomatea, and Spirotrichea were dominant in the three sites. The study discusses the ability of the metabarcoding approach to uncover unknown and rare species. The study highlights the need for refined reference databases and cautious interpretation of the high-throughput sequencing-generated data while emphasizing the complementary nature of molecular and morphological approaches in studying ciliate diversity.
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Affiliation(s)
- Jeeva Susan Abraham
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Sripoorna Somasundaram
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Utkarsh Sood
- Department of Zoology, Kirori Mal College, University of Delhi, Delhi 110007, India
| | - Rup Lal
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Ravi Toteja
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Ciliate Biology Laboratory, Department of Zoology, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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Wang L, Chen X, Pan F, Yao G, Chen J. Development of a rapid detection method for Karenia mikimotoi by using CRISPR-Cas12a. Front Microbiol 2023; 14:1205765. [PMID: 37608945 PMCID: PMC10440436 DOI: 10.3389/fmicb.2023.1205765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Abstract
Harmful algal blooms (HABs), mainly formed by dinoflagellates, have detrimental effects on marine ecosystems and public health. Therefore, detecting HABs is crucial for early warning and prevention of HABs as well as the mitigation of their adverse effects. Although various methods, such as light microscopy, electron microscopy, real-time PCR, and microarrays, have already been established for the detection of HABs, they are still cumbersome to be exploited in the field. Therefore, rapid nucleic detection methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP)-lateral flow dipstick (LFD) have been developed for monitoring bloom-forming algae. However, the CRISPR/Cas-based detection of HABs has yet to be applied to this field. In this study, we developed a method for detecting Karenia mikimotoi (K. mikimotoi), a typical ichthyotoxic dinoflagellate responsible for global blooms. Our method utilized Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) to target and cleave the internal transcribed spacer (ITS) of K. mikimotoi, guided by RNA. We leveraged the target-activated non-specific single-stranded deoxyribonuclease cleavage activity of LbCas12a to generate signals that can be detected using fluorescence-read machines or LFDs. By combining RPA and LbCas12a with reporters, we significantly enhanced the sensitivity, enabling the detection of ITS-harboring plasmids at concentrations as low as 9.8 aM and genomic DNA of K. mikimotoi at levels as low as 3.6 × 10-5 ng/μl. Moreover, we simplified the genomic DNA extraction method using cellulose filter paper (CFP) by directly eluting the DNA into RPA reactions, reducing the extraction time to < 30 s. The entire process, from genomic DNA extraction to result reporting, takes less than an hour, enabling the identification of nearly a single cell. In conclusion, our method provided an easy, specific, and sensitive approach for detecting K. mikimotoi, offering the potential for efficient monitoring and management of K. mikimotoi blooms.
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Affiliation(s)
- Lu Wang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Xiaoyao Chen
- Fishery Resources Monitoring Center of Fujian Province, Fuzhou, China
| | - Feifei Pan
- Fishery Resources Monitoring Center of Fujian Province, Fuzhou, China
| | - Guangshan Yao
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Jianming Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
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Jang SH, Na SI, Lee MJ, Yoo YD. Assessing the utility of mitochondrial gene markers in the family Suessiaceae (Dinophyta) with phylogenomic validation. Mol Phylogenet Evol 2022; 177:107625. [PMID: 36064085 DOI: 10.1016/j.ympev.2022.107625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/13/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
The dinoflagellate family Suessiaceae comprises cosmopolitan species distributed across polar and tropical waters in both marine and freshwater ecosystems, encompassing free-living forms, symbionts, and parasites. Recently, species diversity within the family has rapidly expanded, now including a few species reported to cause red tides. Despite their ecological and evolutionary importance, classifying them within Suessiaceae is difficult due to the limitations of the existing molecular markers-the highly conserved small subunit ribosomal gene (SSU rDNA) and the presence of two indel regions of sequence fragments of the large subunit ribosomal gene (LSU rDNA)-resulting in poorly resolved phylogenetic relationships. We assessed mitochondrial cytochrome b (cob) and cytochrome c oxidase 1 (cox1) genes to develop robust molecular markers that can reveal the genetic diversity of the family Suessiaceae. The divergences of cob and cox1 sequences among the species in the family were greater than the SSU rDNA but less than the LSU rDNA and the ITS region. Moreover, the distinctive topology inferred from the mitochondrial genes provided high resolution among the suessiacean species. We examined the validity of the genetic markers using phylogenomics based on 2,023 core proteins. The divergence of the cob phylogeny was most consistent with that of the phylogenomic results. Taken together, the cob gene can be a novel marker reflecting topology at the genome-scale within the family Suessiaceae.
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Affiliation(s)
- Se Hyeon Jang
- Department of Oceanography, Chonnam National University, Gwangju 61186, South Korea.
| | - Seong In Na
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, South Korea
| | - Moo Joon Lee
- Department of Marine Biotechnology, Anyang University, Incheon 23038, South Korea
| | - Yeong Du Yoo
- Department of Marine Biotechnology, College of Ocean Sciences, Kunsan National University, Kunsan 54150, South Korea
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Zhu CQ, Xu XD, Zhen Y. Systematic review of the firefly genus Emeia Fu, Ballantyne & Lambkin, 2012 (Coleoptera, Lampyridae) from China. Zookeys 2022; 1113:153-166. [PMID: 36762232 PMCID: PMC9848877 DOI: 10.3897/zookeys.1113.79721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/26/2022] [Indexed: 11/12/2022] Open
Abstract
The Luciolinae genus Emeia Fu, Ballantyne & Lambkin, 2012 is reviewed. Phylogenetic relationships based on cox1 DNA barcoding sequences from 42 fireflies and 2 outgroup species are reconstructed. The dataset included three main Lampyridae subfamilies: Luciolinae, Photurinae and Lampyrinae, and Emeia was recovered within Luciolinae. A new species, Emeiapulchra Zhu & Zhen sp. nov., is described from the wetland of Lishui, Zhejiang, China. Emeiapulchra is sister species to E.pseudosauteri from Sichuan, which is supported by morphological characters and a phylogeny based on DNA barcoding sequences. The two species are separated geographically as shown on the distribution map. A key to species of Emeia using males is provided.
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Affiliation(s)
- Cheng-Qi Zhu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ChinaWestlake UniversityHangzhouChina,Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, ChinaZhejiang UniversityHangzhouChina,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, ChinaWestlake Institute for Advanced StudyHangzhouChina
| | - Xiao-Dong Xu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, ChinaZhejiang UniversityHangzhouChina,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, ChinaWestlake Institute for Advanced StudyHangzhouChina
| | - Ying Zhen
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, ChinaZhejiang UniversityHangzhouChina,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, ChinaWestlake Institute for Advanced StudyHangzhouChina
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Zaheri B, Morse D. An overview of transcription in dinoflagellates. Gene 2022; 829:146505. [PMID: 35447242 DOI: 10.1016/j.gene.2022.146505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 02/18/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]
Abstract
Dinoflagellates are a vital diverse family of unicellular algae widespread in various aquatic environments. Typically large genomes and permanently condensed chromosomes without histones make these organisms unique among eukaryotes in terms of chromatin structure and gene expression. Genomic and transcriptomic sequencing projects have provided new insight into the genetic foundation of dinoflagellate behaviors. Genes in tandem arrays, trans-splicing of mRNAs and lower levels of transcriptional regulation compared to other eukaryotes all contribute to the differences seen. Here we present a general overview of transcription in dinoflagellates based on previously described work.
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Affiliation(s)
- Bahareh Zaheri
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke est, Université de Montréal, Montréal H1X 2B2, Canada
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, 4101 Sherbrooke est, Université de Montréal, Montréal H1X 2B2, Canada.
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Ott BM, Litaker RW, Holland WC, Delwiche CF. Using RDNA sequences to define dinoflagellate species. PLoS One 2022; 17:e0264143. [PMID: 35213572 PMCID: PMC8880924 DOI: 10.1371/journal.pone.0264143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
Dinoflagellate species are traditionally defined using morphological characters, but molecular evidence accumulated over the past several decades indicates many morphologically-based descriptions are inaccurate. This recognition led to an increasing reliance on DNA sequence data, particularly rDNA gene segments, in defining species. The validity of this approach assumes the divergence in rDNA or other selected genes parallels speciation events. Another concern is whether single gene rDNA phylogenies by themselves are adequate for delineating species or if multigene phylogenies are required instead. Currently, few studies have directly assessed the relative utility of multigene versus rDNA-based phylogenies for distinguishing species. To address this, the current study examined D1-D3 and ITS/5.8S rDNA gene regions, a multi-gene phylogeny, and morphological characters in Gambierdiscus and other related dinoflagellate genera to determine if they produce congruent phylogenies and identify the same species. Data for the analyses were obtained from previous sequencing efforts and publicly available dinoflagellate transcriptomic libraries as well from the additional nine well-characterized Gambierdiscus species transcriptomic libraries generated in this study. The D1-D3 and ITS/5.8S phylogenies successfully identified the described Gambierdiscus and Alexandrium species. Additionally, the data showed that the D1-D3 and multigene phylogenies were equally capable of identifying the same species. The multigene phylogenies, however, showed different relationships among species and are likely to prove more accurate at determining phylogenetic relationships above the species level. These data indicated that D1-D3 and ITS/5.8S rDNA region phylogenies are generally successful for identifying species of Gambierdiscus, and likely those of other dinoflagellates. To assess how broadly general this finding is likely to be, rDNA molecular phylogenies from over 473 manuscripts representing 232 genera and 863 described species of dinoflagellates were reviewed. Results showed the D1-D3 rDNA and ITS phylogenies in combination are capable of identifying 97% of dinoflagellate species including all the species belonging to the genera Alexandrium, Ostreopsis and Gambierdiscus, although it should be noted that multi-gene phylogenies are preferred for inferring relationships among these species. A protocol is presented for determining when D1-D3, confirmed by ITS/5.8S rDNA sequence data, would take precedence over morphological features when describing new dinoflagellate species. This protocol addresses situations such as: a) when a new species is both morphologically and molecularly distinct from other known species; b) when a new species and closely related species are morphologically indistinguishable, but genetically distinct; and c) how to handle potentially cryptic species and cases where morphotypes are clearly distinct but have the same rDNA sequence. The protocol also addresses other molecular, morphological, and genetic approaches required to resolve species boundaries in the small minority of species where the D1-D3/ITS region phylogenies fail.
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Affiliation(s)
- Brittany M. Ott
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland—College Park, College Park, MD, United States of America
- Cell Biology and Molecular Genetics, University of Maryland—College Park, College Park, MD, United States of America
- * E-mail: (BMO); (RWL)
| | - R. Wayne Litaker
- CSS, Inc. Under Contract to National Oceanic and Atmospheric Administration (NOAA), National Ocean Service, National Centers for Coastal Ocean Science, Beaufort Laboratory, Beaufort, North Carolina, United States of America
- * E-mail: (BMO); (RWL)
| | - William C. Holland
- National Oceanic and Atmospheric Administration, National Ocean Service, National Centers for Coastal Ocean Science, Beaufort Laboratory, Beaufort, North Carolina, United States of America
| | - Charles F. Delwiche
- Cell Biology and Molecular Genetics, University of Maryland—College Park, College Park, MD, United States of America
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Pearson LA, D'Agostino PM, Neilan BA. Recent developments in quantitative PCR for monitoring harmful marine microalgae. HARMFUL ALGAE 2021; 108:102096. [PMID: 34588118 DOI: 10.1016/j.hal.2021.102096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Marine microalgae produce a variety of specialised metabolites that have toxic effects on humans, farmed fish, and marine wildlife. Alarmingly, many of these compounds bioaccumulate in the tissues of shellfish and higher trophic organisms, including species consumed by humans. Molecular methods are emerging as a potential alternative and complement to the conventional microscopic diagnosis of toxic or otherwise harmful microalgal species. Quantitative PCR (qPCR) in particular, has gained popularity over the past decade as a sensitive, rapid, and cost-effective method for monitoring harmful microalgae. Assays targeting taxonomic marker genes provide the opportunity to identify and quantify (or semi-quantify) microalgal species and importantly to pre-empt bloom events. Moreover, the discovery of paralytic shellfish toxin biosynthesis genes in dinoflagellates has enabled researchers to directly monitor toxigenic species in coastal waters and fisheries. This review summarises the recent developments in qPCR detection methods for harmful microalgae, with emphasis on emerging toxin gene monitoring technologies.
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Affiliation(s)
- Leanne A Pearson
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Paul M D'Agostino
- Chair of Technical Biochemistry, Technical University of Dresden, Dresden, Germany
| | - Brett A Neilan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia.
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Suarez-Menendez M, Planes S, Garcia-Vazquez E, Ardura A. Early Alert of Biological Risk in a Coastal Lagoon Through eDNA Metabarcoding. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Park JH, Kim M, Jeong HJ, Park MG. Revisiting the taxonomy of the "Dinophysis acuminata complex'' (Dinophyta)'. HARMFUL ALGAE 2019; 88:101657. [PMID: 31582152 DOI: 10.1016/j.hal.2019.101657] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/05/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Marine dinoflagellates of the genus Dinophysis are well known for producing diarrhetic shellfish poisoning (DSP) toxins and/or pectenotoxins which have a significant impact on public health as well as on marine aquaculture. Out of more than 80 Dinophysis species recorded so far, D. cf. acuminata is the most commonly observed in coastal areas worldwide. Due to their highly similar morphological features, however, an accurate discrimination of the various D. cf. acuminata species such as D. acuminata, D. ovum, and D. sacculus under light microscopy has proven to be a difficult task to accomplish. Hence, these species have thus far been referred to as the "Dinophysis acuminata complex". Recent studies showed a discrimination between local strains of D. acuminata and D. ovum from Galician, northwestern Spain, using the mitochondrial cox1 gene as a genetic marker in addition to commonly used morphological features such as size and contour of the large hypothecal plates, shape of the small cells formed as part of their polymorphic life-cycle, development of the left sulcal list and ribs, and length of the right sulcal list. In the present study, attempts were made to discriminate between D. acuminata and D. ovum following single-cell isolation of 54 "D. acuminata complex" collected from Korean coastal waters, based on the abovementioned traits. Morphological data showed that all the traits analyzed overlapped between the two species. The mitochondrial cox1 (cytochrome c oxidase subunit I) gene sequences of every isolate were also determined, but a genetic distinction between D. acuminata and D. ovum could not be confirmed, suggesting that the cox1 gene is not a suitable genetic marker for discrimination between the two species. The results of this study suggest that the morphological variations observed within the "D. acuminata complex" may have been caused by several factors (e.g. different geographical locations, seasonal changes, and different environmental conditions), and that D. acuminata and D. ovum may be the same species.
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Affiliation(s)
- Jeong Ha Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Miran Kim
- Research Institute for Basic Sciences, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Myung Gil Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju 61186, Republic of Korea
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Discovery of a New Clade Nested Within the Genus Alexandrium (Dinophyceae): Morpho-molecular Characterization of Centrodinium punctatum (Cleve) F.J.R. Taylor. Protist 2019; 170:168-186. [DOI: 10.1016/j.protis.2019.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 11/22/2022]
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13
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John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K, Glöckner G. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. SCIENCE ADVANCES 2019; 5:eaav1110. [PMID: 31032404 PMCID: PMC6482013 DOI: 10.1126/sciadv.aav1110] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/07/2019] [Indexed: 05/30/2023]
Abstract
Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.
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Affiliation(s)
- Uwe John
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Yameng Lu
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sylke Wohlrab
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gurjeet S. Kohli
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Felix C. Mark
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Sarah Farhat
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Marius Felder
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Stephan Frickenhaus
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Hochschule Bremerhaven, Bremerhaven, Germany
| | - Laure Guillou
- CNRS, UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 6, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
| | - Patrick J. Keeling
- Botany Department, University of British Columbia, Vancouver, BC, Canada
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Betina M. Porcel
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Klaus Valentin
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Gernot Glöckner
- Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
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Annenkova NV, Ahrén D, Logares R, Kremp A, Rengefors K. Delineating closely related dinoflagellate lineages using phylotranscriptomics. JOURNAL OF PHYCOLOGY 2018; 54:571-576. [PMID: 29676790 DOI: 10.1111/jpy.12748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Recently radiated dinoflagellates Apocalathium aciculiferum (collected in Lake Erken, Sweden), Apocalathium malmogiense (Baltic Sea) and Apocalathium aff. malmogiense (Highway Lake, Antarctica) represent a lineage with an unresolved phylogeny. We determined their phylogenetic relationships using phylotranscriptomics based on 792 amino acid sequences. Our results showed that A. aciculiferum diverged from the other two closely related lineages, consistent with their different morphologies in cell size, relative cell length and presence of spines. We hypothesized that A. aff. malmogiense and A. malmogiense, which inhabit different hemispheres, are evolutionarily more closely related because they diverged from a marine common ancestor, adapting to a wide salinity range, while A. aciculiferum colonized a freshwater habitat, by acquiring adaptations to this environment, in particular, salinity intolerance. We show that phylotranscriptomics can resolve the phylogeny of recently diverged protists. This has broad relevance, given that many phytoplankton species are morphologically very similar, and single genes sometimes lack the information to determine species' relationships.
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Affiliation(s)
- Nataliia V Annenkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences 3, Ulan-Batorskaya St., 664033, Irkutsk, Russia
| | - Dag Ahrén
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
- Bioinformatics Infrastructures for Life Sciences (BILS), Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Science (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim de la Barceloneta 37-49, E08003, Barcelona, Spain
| | - Anke Kremp
- Marine Research Centre, Finnish Environment Institute, Erik Palmenin aukio 1, 00560, Helsinki, Finland
| | - Karin Rengefors
- Aquatic Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
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15
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Sze Y, Miranda LN, Sin TM, Huang D. Characterising planktonic dinoflagellate diversity in Singapore using DNA metabarcoding. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.25136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dinoflagellates are traditionally identified morphologically using microscopy, which is a time-consuming and labour-intensive process. Hence, we explored DNA metabarcoding using high-throughput sequencing as a more efficient way to study planktonic dinoflagellate diversity in Singapore’s waters. From 29 minimally pre-sorted water samples collected at four locations in western Singapore, DNA was extracted, amplified and sequenced for a 313-bp fragment of the V4–V5 region in the 18S ribosomal RNA gene. Two sequencing runs generated 2,847,170 assembled paired-end reads, corresponding to 573,176 unique sequences. Sequences were clustered at 97% similarity and analysed with stringent thresholds (≥150 bp, ≥20 reads, ≥95% match to dinoflagellates), recovering 28 dinoflagellate taxa. Dinoflagellate diversity captured includes parasitic and symbiotic groups which are difficult to identify morphologically. Richness is similar between the inner and outer West Johor Strait, but variations in community structure are apparent, likely driven by environmental differences. None of the taxa detected in a recent phytoplankton bloom along the West Johor Strait have been recovered in our samples, suggesting that background communities are distinct from bloom communities. The voluminous data obtained in this study contribute baseline information for Singapore’s phytoplankton communities and prompt future research and monitoring to adopt the approach established here.
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16
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Mendizabal-Ruiz G, Román-Godínez I, Torres-Ramos S, Salido-Ruiz RA, Vélez-Pérez H, Morales JA. Genomic signal processing for DNA sequence clustering. PeerJ 2018; 6:e4264. [PMID: 29379686 PMCID: PMC5786891 DOI: 10.7717/peerj.4264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/24/2017] [Indexed: 11/20/2022] Open
Abstract
Genomic signal processing (GSP) methods which convert DNA data to numerical values have recently been proposed, which would offer the opportunity of employing existing digital signal processing methods for genomic data. One of the most used methods for exploring data is cluster analysis which refers to the unsupervised classification of patterns in data. In this paper, we propose a novel approach for performing cluster analysis of DNA sequences that is based on the use of GSP methods and the K-means algorithm. We also propose a visualization method that facilitates the easy inspection and analysis of the results and possible hidden behaviors. Our results support the feasibility of employing the proposed method to find and easily visualize interesting features of sets of DNA data.
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Affiliation(s)
| | - Israel Román-Godínez
- Departamento de Ciencias Computacionales, Universidad de Guadalajara, Guadalajara, Mexico
| | - Sulema Torres-Ramos
- Departamento de Ciencias Computacionales, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ricardo A Salido-Ruiz
- Departamento de Ciencias Computacionales, Universidad de Guadalajara, Guadalajara, Mexico
| | - Hugo Vélez-Pérez
- Departamento de Ciencias Computacionales, Universidad de Guadalajara, Guadalajara, Mexico
| | - J Alejandro Morales
- Departamento de Ciencias Computacionales, Universidad de Guadalajara, Guadalajara, Mexico
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Park BS, Kim JH, Kim JH, Baek SH, Han MS. Intraspecific bloom succession in the harmful dinoflagellate Cochlodinium polykrikoides (Dinophyceae) extended the blooming period in Korean coastal waters in 2009. HARMFUL ALGAE 2018; 71:78-88. [PMID: 29306398 DOI: 10.1016/j.hal.2017.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 11/03/2017] [Accepted: 12/08/2017] [Indexed: 06/07/2023]
Abstract
Although there have been extensive studies on dinoflagellate blooms in recent decades, the mechanism that allows the maintenance of blooms over long periods remains uncertain, and studies on genetically differentiated subpopulations may provide insights into this mechanism. In this study, the influence of two genetically distinct subpopulations of the dinoflagellate Cochlodinium polykrikoides, referred to as Group I and IV, on bloom duration in Korean coastal waters (KCW) was examined using a quantitative PCR (qPCR) assay. In this study, a C. polykrikoides bloom occurred over a longer period in 2009 (49 days), whereas the bloom period was shorter in 2010 (35 days). The qPCR results indicate that intraspecific bloom succession between Groups I and IV occurred in 2009, whereas only a single subpopulation (Group I) was responsible for the bloom in 2010. Based on the statistical analysis, the Group I and Group IV blooms occurred under significantly different environmental conditions (p ≤ 0.05) in terms of water temperature, pH, and phosphate concentration, and these subpopulations exhibited significantly different relationships with environmental factors, particularly water temperature (p < 0.01). This variability may allow blooms to continue through intraspecific bloom succession even after environmental conditions change. Southern KCW are affected by outer regions via the Tsushima Warm Current (TWC) every summer. Group IV (≤1108 ± 69 cells L-1) was primarily observed along the route of the TWC in summer 2009, when the bloom of this subpopulation occurred in southern KCW. These results suggest that Group IV transported via the TWC may have influenced the bloom dynamics of this subpopulation in summer 2009.
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Affiliation(s)
- Bum Soo Park
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Jin Ho Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Joo-Hwan Kim
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Seung Ho Baek
- South Sea Research Institute, Korea Institute of Ocean Science & Technology, Geoje 53201, South Korea
| | - Myung-Soo Han
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, South Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 04763, South Korea.
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18
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Gao Y, Fang H, Dong Y, Li H, Pu C, Zhan A. An improved method for the molecular identification of single dinoflagellate cysts. PeerJ 2017; 5:e3224. [PMID: 28462033 PMCID: PMC5408718 DOI: 10.7717/peerj.3224] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Dinoflagellate cysts (i.e., dinocysts) are biologically and ecologically important as they can help dinoflagellate species survive harsh environments, facilitate their dispersal and serve as seeds for harmful algal blooms. In addition, dinocysts derived from some species can produce more toxins than vegetative forms, largely affecting species through their food webs and even human health. Consequently, accurate identification of dinocysts represents the first crucial step in many ecological studies. As dinocysts have limited or even no available taxonomic keys, molecular methods have become the first priority for dinocyst identification. However, molecular identification of dinocysts, particularly when using single cells, poses technical challenges. The most serious is the low success rate of PCR, especially for heterotrophic species. METHODS In this study, we aim to improve the success rate of single dinocyst identification for the chosen dinocyst species (Gonyaulax spinifera, Polykrikos kofoidii, Lingulodinium polyedrum, Pyrophacus steinii, Protoperidinium leonis and Protoperidinium oblongum) distributed in the South China Sea. We worked on two major technical issues: cleaning possible PCR inhibitors attached on the cyst surface and designing new dinoflagellate-specific PCR primers to improve the success of PCR amplification. RESULTS For the cleaning of single dinocysts separated from marine sediments, we used ultrasonic wave-based cleaning and optimized cleaning parameters. Our results showed that the optimized ultrasonic wave-based cleaning method largely improved the identification success rate and accuracy of both molecular and morphological identifications. For the molecular identification with the newly designed dinoflagellate-specific primers (18S634F-18S634R), the success ratio was as high as 86.7% for single dinocysts across multiple taxa when using the optimized ultrasonic wave-based cleaning method, and much higher than that (16.7%) based on traditional micropipette-based cleaning. DISCUSSION The technically simple but robust method improved on in this study is expected to serve as a powerful tool in deep understanding of population dynamics of dinocysts and the causes and consequences of potential negative effects caused by dinocysts.
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Affiliation(s)
- Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hongda Fang
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Yanhong Dong
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Haitao Li
- South China Sea Environmental Monitoring Center, State Oceanic Administration, Guangzhou, China
| | - Chuanliang Pu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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19
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Krayesky-Self S, Schmidt WE, Phung D, Henry C, Sauvage T, Camacho O, Felgenhauer BE, Fredericq S. Eukaryotic Life Inhabits Rhodolith-forming Coralline Algae (Hapalidiales, Rhodophyta), Remarkable Marine Benthic Microhabitats. Sci Rep 2017; 7:45850. [PMID: 28368049 PMCID: PMC5377461 DOI: 10.1038/srep45850] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/03/2017] [Indexed: 11/21/2022] Open
Abstract
Rhodoliths are benthic calcium carbonate nodules accreted by crustose coralline red algae which recently have been identified as useful indicators of biomineral changes resulting from global climate change and ocean acidification. This study highlights the discovery that the interior of rhodoliths are marine biodiversity hotspots that function as seedbanks and temporary reservoirs of previously unknown stages in the life history of ecologically important dinoflagellate and haptophyte microalgae. Whereas the studied rhodoliths originated from offshore deep bank pinnacles in the northwestern Gulf of Mexico, the present study opens the door to assess the universality of endolithic stages among bloom-forming microalgae spanning different phyla, some of public health concerns (Prorocentrum) in marine ecosystems worldwide.
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Affiliation(s)
| | - William E Schmidt
- University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
| | - Delena Phung
- University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
| | - Caroline Henry
- University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
| | - Thomas Sauvage
- University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA.,Smithsonian Marine Station at Fort Pierce, Fort Pierce, Florida, 34949, USA
| | - Olga Camacho
- University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
| | | | - Suzanne Fredericq
- University of Louisiana at Lafayette, Lafayette, Louisiana, 70504-3602, USA
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20
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Deng Y, Zhang Q, Ming R, Lin L, Lin X, Lin Y, Li X, Xie B, Wen Z. Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi. Int J Mol Sci 2016; 17:ijms17071049. [PMID: 27376282 PMCID: PMC4964425 DOI: 10.3390/ijms17071049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/29/2022] Open
Abstract
Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification.
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Affiliation(s)
- Youjin Deng
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Qihui Zhang
- Gutian Edible Fungal Research and Development Center, Ningde 352200, China.
| | - Ray Ming
- Gutian Edible Fungal Research and Development Center, Ningde 352200, China.
| | - Longji Lin
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xiangzhi Lin
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yiying Lin
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xiao Li
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Baogui Xie
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhiqiang Wen
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Le Bescot N, Mahé F, Audic S, Dimier C, Garet MJ, Poulain J, Wincker P, de Vargas C, Siano R. Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding. Environ Microbiol 2015; 18:609-26. [DOI: 10.1111/1462-2920.13039] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Noan Le Bescot
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Frédéric Mahé
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
- Department of Ecology; Technische Universität Kaiserslautern; Erwin-Schrödinger Str. 14 D-67663 Kaiserslautern Germany
| | - Stéphane Audic
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Céline Dimier
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Marie-José Garet
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Julie Poulain
- Centre National de Séquençage; CEA-Institut de Génomique, GENOSCOPE; Evry Cedex France
| | - Patrick Wincker
- Centre National de Séquençage; CEA-Institut de Génomique, GENOSCOPE; Evry Cedex France
- Université d'Evry, UMR 8030; rue Gaston Crémieux CP5706 91057 Evry Cedex France
- Centre National de la Recherche Scientifique (CNRS), UMR 8030; rue Gaston Crémieux CP5706 91057 Evry Cedex France
| | - Colomban de Vargas
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
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22
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Kosakyan A, Mulot M, Mitchell EAD, Lara E. Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae). Eur J Protistol 2015. [PMID: 26196835 DOI: 10.1016/j.ejop.2015.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.
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Affiliation(s)
- Anush Kosakyan
- Laboratory of Soil Biology, University of Neuchatel, Rue Emile-Argand 11, CH-2000 Neuchatel, Switzerland; Institute of Biosciences, Department of Zoology, University of Sao Paulo, Rua do Matão, Travessa 14, Cidade Universitária, 05508-090 - Sao Paulo, SP, Brasil.
| | - Matthieu Mulot
- Laboratory of Soil Biology, University of Neuchatel, Rue Emile-Argand 11, CH-2000 Neuchatel, Switzerland
| | - Edward A D Mitchell
- Laboratory of Soil Biology, University of Neuchatel, Rue Emile-Argand 11, CH-2000 Neuchatel, Switzerland; Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, CH-2000 Neuchâtel, Switzerland
| | - Enrique Lara
- Laboratory of Soil Biology, University of Neuchatel, Rue Emile-Argand 11, CH-2000 Neuchatel, Switzerland
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Herrera-Sepúlveda A, Medlin LK, Murugan G, Sierra-Beltrán AP, Cruz-Villacorta AA, Hernández-Saavedra NY. Are Prorocentrum hoffmannianum and Prorocentrum belizeanum (DINOPHYCEAE, PROROCENTRALES), the same species? An integration of morphological and molecular data. JOURNAL OF PHYCOLOGY 2015; 51:173-188. [PMID: 26986267 DOI: 10.1111/jpy.12265] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/05/2014] [Indexed: 06/05/2023]
Abstract
The taxonomic assignment of Prorocentrum species is based on morphological characteristics; however, morphological variability has been found for several taxa isolated from different geographical regions. In this study, we evaluated species boundaries of Prorocentrum hoffmannianum and Prorocentrum belizeanum based on morphological and molecular data. A detailed morphological analysis was done, concentrating on the periflagellar architecture. Molecular analyses were performed on partial Small Sub-Unit (SSU) rDNA, partial Large Sub-Unit (LSU) rDNA, complete Internal Transcribed Spacer Regions (ITS1-5.8S-ITS2), and partial cytochrome b (cob) sequences. We concatenated the SSU-ITS-LSU fragments and constructed a phylogenetic tree using Bayesian Inference (BI) and maximum likelihood (ML) methods. Morphological analyses indicated that the main characters, such as cell size and number of depressions per valve, normally used to distinguish P. hoffmannianum from P. belizeanum, overlapped. No clear differences were found in the periflagellar area architecture. Prorocentrum hoffmannianum and P. belizeanum were a highly supported monophyletic clade separated into three subclades, which broadly corresponded to the sample collection regions. Subtle morphological overlaps found in cell shape, size, and ornamentation lead us to conclude that P. hoffmanianum and P. belizeanum might be considered conspecific. The molecular data analyses did not separate P. hoffmannianum and P. belizeanum into two morphospecies, and thus, we considered them to be the P. hoffmannianum species complex because their clades are separated by their geographic origin. These geographic and genetically distinct clades could be referred to as ribotypes: (A) Belize, (B) Florida-Cuba, (C1) India, and (C2) Australia.
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Affiliation(s)
- Angélica Herrera-Sepúlveda
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
| | - Linda K Medlin
- Marine Biological Association of the UK, The Citadel, Plymouth, PL1 2BP, UK
| | - Gopal Murugan
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
| | - Arturo P Sierra-Beltrán
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
| | - Ariel A Cruz-Villacorta
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
| | - Norma Y Hernández-Saavedra
- Centro de Investigaciones Biológicas del Noroeste S. C., Avenida Instituto Politécnico Nacional 195, La Paz, BCS 23090, México
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24
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Recent radiation in a marine and freshwater dinoflagellate species flock. ISME JOURNAL 2015; 9:1821-34. [PMID: 25603395 DOI: 10.1038/ismej.2014.267] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/03/2014] [Accepted: 12/12/2014] [Indexed: 11/09/2022]
Abstract
Processes of rapid radiation among unicellular eukaryotes are much less studied than among multicellular organisms. We have investigated a lineage of cold-water microeukaryotes (protists) that appear to have diverged recently. This lineage stands in stark contrast to known examples of phylogenetically closely related protists, in which genetic difference is typically larger than morphological differences. We found that the group not only consists of the marine-brackish dinoflagellate species Scrippsiella hangoei and the freshwater species Peridinium aciculiferum as discovered previously but also of a whole species flock. The additional species include Peridinium euryceps and Peridinium baicalense, which are restricted to a few lakes, in particular to the ancient Lake Baikal, Russia, and freshwater S. hangoei from Lake Baikal. These species are characterized by relatively large conspicuous morphological differences, which have given rise to the different species descriptions. However, our scanning electron microscopic studies indicate that they belong to a single genus according to traditional morphological characterization of dinoflagellates (thecal plate patterns). Moreover, we found that they have identical SSU (small subunit) rDNA fragments and distinct but very small differences in the DNA markers LSU (large subunit) rDNA, ITS2 (internal transcribed spacer 2) and COB (cytochrome b) gene, which are used to delineate dinoflagellates species. As some of the species co-occur, and all four have small but species-specific sequence differences, we suggest that these taxa are not a case of phenotypic plasticity but originated via recent adaptive radiation. We propose that this is the first clear example among free-living microeukaryotes of recent rapid diversification into several species followed by dispersion to environments with different ecological conditions.
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25
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Casabianca S, Perini F, Casabianca A, Battocchi C, Giussani V, Chiantore M, Penna A. Monitoring toxic Ostreopsis cf. ovata in recreational waters using a qPCR based assay. MARINE POLLUTION BULLETIN 2014; 88:102-109. [PMID: 25282181 DOI: 10.1016/j.marpolbul.2014.09.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/05/2014] [Accepted: 09/06/2014] [Indexed: 06/03/2023]
Abstract
Ostreopsis sp. is a toxic marine benthic dinoflagellate that causes high biomass blooms, posing a threat to human health, marine biota and aquaculture activities, and negatively impacting coastal seawater quality. Species-specific identification and enumeration is fundamental because it can allow the implementation of all the necessary preventive measures to properly manage Ostreopsis spp. bloom events in recreational waters and aquaculture farms. The aim of this study was to apply a rapid and sensitive qPCR method to quantify Ostreopsis cf. ovata abundance in environmental samples collected from Mediterranean coastal sites and to develop site-specific environmental standard curves. Similar PCR efficiencies of plasmid and environmental standard curves allowed us to estimate the LSU rDNA copy number per cell. Moreover, we assessed the effectiveness of mitochondrial COI and cob genes as alternative molecular markers to ribosomal genes in qPCR assays for Ostreopsis spp. quantification.
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Affiliation(s)
- Silvia Casabianca
- Section of Environmental Biology, Dep. of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy
| | - Federico Perini
- Section of Environmental Biology, Dep. of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy
| | - Anna Casabianca
- Section of Environmental Biology, Dep. of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy
| | - Cecilia Battocchi
- Section of Environmental Biology, Dep. of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy
| | - Valentina Giussani
- Department of Earth, Environment and Life Sciences, University of Genoa, Corso Europa 26, 16132 Genoa, Italy
| | - Mariachiara Chiantore
- Department of Earth, Environment and Life Sciences, University of Genoa, Corso Europa 26, 16132 Genoa, Italy
| | - Antonella Penna
- Section of Environmental Biology, Dep. of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy; ISMAR CNR, Largo Fiera della Pesca, 60125 Ancona, Italy.
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26
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Chong J, Jackson C, Kim JI, Yoon HS, Reyes-Prieto A. Molecular markers from different genomic compartments reveal cryptic diversity within glaucophyte species. Mol Phylogenet Evol 2014; 76:181-8. [DOI: 10.1016/j.ympev.2014.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 03/14/2014] [Accepted: 03/18/2014] [Indexed: 11/29/2022]
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27
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Tekle YI. DNA barcoding in amoebozoa and challenges: the example of Cochliopodium. Protist 2014; 165:473-84. [PMID: 24945930 DOI: 10.1016/j.protis.2014.05.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/15/2014] [Accepted: 05/17/2014] [Indexed: 11/29/2022]
Abstract
The diversity of microbial eukaryotes in general and amoeboid lineages in particular is poorly documented. Even though amoeboid lineages are among the most abundant microbes, taxonomic progress in the group has been hindered by the limitations of traditional taxonomy and technical difficultly in studying them. Studies using molecular approaches such as DNA barcoding with cytochrome oxidase I (COI) gene are slowly trickling in for Amoebozoa, and they hopefully will aid in unveiling the true diversity of the group. In this study a retrospective approach is used to test the utility of COI gene in a scale-bearing amoeba, Cochliopodium, which is morphologically well defined. A total of 126 COI sequences and 62 unique haplotypes were generated from 9 Cochliopodium species. Extensive analyses exploring effects of sequence evolution models and length of sequence on genetic diversity computations were conducted. The findings show that COI is a promising marker for Cochliopodium, except in one case where it failed to delineate two morphologically well-defined cochliopodiums. Two species delimitation approaches also recognize 8 genetic lineages out of 9 species examined. The taxonomic implications of these findings and factors that may confound COI as a barcode marker in Cochliopodium and other amoebae are discussed.
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Affiliation(s)
- Yonas I Tekle
- Spelman College, 350 Spelman Lane Southwest, Atlanta, GA 30314, USA
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28
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Murray SA, Hoppenrath M, Orr RJS, Bolch C, John U, Diwan R, Yauwenas R, Harwood T, de Salas M, Neilan B, Hallegraeff G. Alexandrium diversaporum sp. nov., a new non-saxitoxin producing species: Phylogeny, morphology and sxtA genes. HARMFUL ALGAE 2014; 31:54-65. [PMID: 28040111 DOI: 10.1016/j.hal.2013.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/16/2013] [Accepted: 09/16/2013] [Indexed: 06/06/2023]
Abstract
Species of the PST producing planktonic marine dinoflagellate genus Alexandrium have been intensively scrutinised, and it is therefore surprising that new taxa can still be found. Here we report a new species, Alexandrium diversaporum nov. sp., isolated from spherical cysts found at two sites in Tasmania, Australia. This species differs in its morphology from all previously reported Alexandrium species, possessing a unique combination of morphological features: the presence of 2 size classes of thecal pores on the cell surface, a medium cell size, the size and shape of the 6″, 1', 2⁗ and Sp plates, the lack of a ventral pore, a lack of anterior and posterior connecting pores, and a lack of chain formation. We determined the relationship of the two strains to other species of Alexandrium based on an alignment of concatenated SSU-ITS1, 5.8S, ITS2 and partial LSU ribosomal RNA sequences, and found A. diversaporum to be a sister group to Alexandrium leei with high support. A. leei shares several morphological features, including the relative size and shapes of the 6″, 1', 2⁗ and Sp plates and the fact that some strains of A. leei have two size classes of thecal pores. We examined A. diversaporum strains for saxitoxin production and found them to be non-toxic. The species lacked sequences for the domain A4 of sxtA, as has been previously found for non-saxitoxin producing species of Alexandrium.
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Affiliation(s)
- Shauna A Murray
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Mona Hoppenrath
- Senckenberg Research Institute, Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany
| | - Russell J S Orr
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Christopher Bolch
- National Centre for Marine Conservation and Resource Sustainability, Australian Maritime College, University of Tasmania, Locked Bag 1370, Launceston, Tasmania 7250, Australia
| | - Uwe John
- Section Ecological Chemistry, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Rutuja Diwan
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia
| | - Rouna Yauwenas
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia
| | - Tim Harwood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Miguel de Salas
- Tasmanian Herbarium, University of Tasmania, Private Bag 4, Hobart, Tasmania 7001, Australia
| | - Brett Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Gustaaf Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
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29
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Wang L, Zhuang Y, Zhang H, Lin X, Lin S. DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species. HARMFUL ALGAE 2014; 31:100-113. [PMID: 28040099 DOI: 10.1016/j.hal.2013.10.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/06/2013] [Accepted: 10/07/2013] [Indexed: 06/06/2023]
Abstract
Alexandrium species can be very difficult to identify, with A. catenella, A. tamarense, and A. fundyense that compose "Alexandrium tamarense species complex" (Atama complex) as a distinct example. DNA barcoding is promising to offer a solution but remains to be established. In this study, we examined the utility of ITS in resolving the Atama species complex, by analyzing previously studied strains plus unstudied Chinese strains within the LSU- and SSU-rDNA based group/clade frameworks recently established. We further investigated the presence of intragenomic polymorphism and its implications in species delimitation. Similar to the previous SSU and LSU results, our ITS-based phylogenies divided the complex to five clusters, but with longer and evener branch lengths between the clusters. Based on the ITS region, the inter-cluster genetic distances (p=0.134-0.216) were consistently and substantially greater than intra-cluster genetic distances (p=0.000-0.066), with an average inter-cluster (species) distance (p=0.167) 7.6-fold of the average intraspecific difference (p=0.022), qualifying the approximately 510-520bp ITS as a DNA barcode for Atama complex. We detected varying levels of intragenomic polymorphism in ITS but found that this did not impact the taxon-resolving power of this gene. With this DNA barcode, the new East and South China Sea strains and one Antarctic strain were placed in Clade IIC/Group IV, even though there were 7-10 polymorphic sites in their ITS, in contrast to none in SSU. Furthermore, our results suggest that the five clusters are recognizable as distinct species according to the phylogenetic species concept. Based on the phylogenetic placements of the type-locality strains of the existing three morphospecies and the dominant localities of other strains, we propose that Group I/Clade I be designated as A. fundyense, Group III/Clade IIB as A. tamarense, Group IV/Clade IIC as A. catenella, Group II/Clade IIA as A. mediterranis, and Group V/Clade IID as A. australis.
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Affiliation(s)
- Lu Wang
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Yunyun Zhuang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Xin Lin
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Senjie Lin
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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30
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Valiadi M, Iglesias-Rodriguez MD. Diversity of the luciferin binding protein gene in bioluminescent dinoflagellates--insights from a new gene in Noctiluca scintillans and sequences from gonyaulacoid genera. J Eukaryot Microbiol 2013; 61:134-45. [PMID: 24373055 DOI: 10.1111/jeu.12091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 12/10/2013] [Accepted: 10/13/2013] [Indexed: 11/30/2022]
Abstract
Dinoflagellate bioluminescence systems operate with or without a luciferin binding protein, representing two distinct modes of light production. However, the distribution, diversity, and evolution of the luciferin binding protein gene within bioluminescent dinoflagellates are not well known. We used PCR to detect and partially sequence this gene from the heterotrophic dinoflagellate Noctiluca scintillans and a group of ecologically important gonyaulacoid species. We report an additional luciferin binding protein gene in N. scintillans which is not attached to luciferase, further to its typical combined bioluminescence gene. This supports the hypothesis that a profound re-organization of the bioluminescence system has taken place in this organism. We also show that the luciferin binding protein gene is present in the genera Ceratocorys, Gonyaulax, and Protoceratium, and is prevalent in bioluminescent species of Alexandrium. Therefore, this gene is an integral component of the standard molecular bioluminescence machinery in dinoflagellates. Nucleotide sequences showed high within-strain variation among gene copies, revealing a highly diverse gene family comprising multiple gene types in some organisms. Phylogenetic analyses showed that, in some species, the evolution of the luciferin binding protein gene was different from the organism's general phylogenies, highlighting the complex evolutionary history of dinoflagellate bioluminescence systems.
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Affiliation(s)
- Martha Valiadi
- Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, UK
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31
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Jeong HJ, Lee SY, Kang NS, Yoo YD, Lim AS, Lee MJ, Kim HS, Yih W, Yamashita H, LaJeunesse TC. Genetics and Morphology Characterize the Dinoflagellate Symbiodinium voratum
, n. sp., (Dinophyceae) as the Sole Representative of Symbiodinium
Clade E. J Eukaryot Microbiol 2013; 61:75-94. [DOI: 10.1111/jeu.12088] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/10/2013] [Accepted: 10/01/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Hae Jin Jeong
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Sung Yeon Lee
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Nam Seon Kang
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Yeong Du Yoo
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - An Suk Lim
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Moo Joon Lee
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Hyung Seop Kim
- Department of Oceanography; Kunsan National University; Kunsan 573-701 Korea
| | - Wonho Yih
- Department of Oceanography; Kunsan National University; Kunsan 573-701 Korea
| | - Hiroshi Yamashita
- Seikai National Fisheries Research Institute; Fisheries Research Agency; Fukai-Ohta; Ishigaki Okinawa 907-0451 Japan
| | - Todd C. LaJeunesse
- Department of Biology; 327 Mueller Laboratory; Pennsylvania State University; University Park PA 16802 USA
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32
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Kohli GS, Neilan BA, Brown MV, Hoppenrath M, Murray SA. Cobgene pyrosequencing enables characterization of benthic dinoflagellate diversity and biogeography. Environ Microbiol 2013; 16:467-85. [DOI: 10.1111/1462-2920.12275] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 09/01/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Gurjeet S. Kohli
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
- Plant Functional Biology and Climate Change Cluster (C3); University of Technology Sydney; Sydney New South Wales 2007 Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
- Australian Centre for Astrobiology; University of New South Wales; Sydney New South Wales 2052 Australia
| | - Mark V. Brown
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
- Australian Centre for Astrobiology; University of New South Wales; Sydney New South Wales 2052 Australia
| | - Mona Hoppenrath
- Senckenberg am Meer; Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB); Wilhelmshaven 32689 Germany
| | - Shauna A. Murray
- Sydney Institute of Marine Sciences; Sydney New South Wales 2088 Australia
- Plant Functional Biology and Climate Change Cluster (C3); University of Technology Sydney; Sydney New South Wales 2007 Australia
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Kurobe T, Baxa DV, Mioni CE, Kudela RM, Smythe TR, Waller S, Chapman AD, Teh SJ. Identification of harmful cyanobacteria in the Sacramento-San Joaquin Delta and Clear Lake, California by DNA barcoding. SPRINGERPLUS 2013; 2:491. [PMID: 24133644 PMCID: PMC3797325 DOI: 10.1186/2193-1801-2-491] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 09/24/2013] [Indexed: 12/04/2022]
Abstract
Accurate identification of cyanobacteria using traditional morphological taxonomy is challenging due to the magnitude of phenotypic plasticity among natural algal assemblages. In this study, molecular approach was utilized to facilitate the accurate identification of cyanobacteria in the Sacramento-San Joaquin Delta and in Clear Lake in Northern California where recurring blooms have been observed over the past decades. Algal samples were collected from both water bodies in 2011 and the samples containing diverse cyanobacteria as identified by morphological taxonomy were chosen for the molecular analysis. The 16S ribosomal RNA genes (16S rDNA) and the adjacent internal transcribed spacer (ITS) regions were amplified by PCR from the mixed algal samples using cyanobacteria generic primers. The obtained sequences were analyzed by similarity search (BLASTN) and phylogenetic analysis (16S rDNA) to differentiate species sharing significantly similar sequences. A total of 185 plasmid clones were obtained of which 77 were successfully identified to the species level: Aphanizomenon flos-aquae, Dolichospermum lemmermannii (taxonomic synonym: Anabaena lemmermannii), Limnoraphis robusta (taxonomic synonym: Lyngbya hieronymusii f. robusta) and Microcystis aeruginosa. To date, Dolichospermum and Limnoraphis found in Clear Lake have only been identified to the genus lavel by microscopy. During the course of this study, morphological identification and DNA barcoding confirmed A. flos-aquae as the predominant cyanobacterium in the Sacramento-San Joaquin Delta indicating a shift from M. aeruginosa that have dominated the blooms in the past decade. Lastly, the species-specific identification of Limnoraphis robusta in Clear Lake is another significant finding as this cyanobacterium has, thus far, only been reported in Lake Atitlan blooms in Guatemala.
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Affiliation(s)
| | | | - Cécile E Mioni
- />California Department of Water Resources, Environmental Monitoring Program, West Sacramento, CA 95691 USA
| | - Raphael M Kudela
- />California Department of Water Resources, Environmental Monitoring Program, West Sacramento, CA 95691 USA
| | | | - Scott Waller
- />California Department of Water Resources, Environmental Monitoring Program, West Sacramento, CA 95691 USA
| | | | - Swee J Teh
- />Greenwater Laboratories, Palatka, FL 32177 USA
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Qiu D, Huang L, Liu S, Zhang H, Lin S. Apical groove type and molecular phylogeny suggests reclassification of Cochlodinium geminatum as Polykrikos geminatum. PLoS One 2013; 8:e71346. [PMID: 23990946 PMCID: PMC3747182 DOI: 10.1371/journal.pone.0071346] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/30/2013] [Indexed: 11/23/2022] Open
Abstract
Traditionally Cocholodinium and Gymnodinium sensu lato clade are distinguished based on the cingulum turn number, which has been increasingly recognized to be inadequate for Gymnodiniales genus classification. This has been improved by the combination of the apical groove characteristics and molecular phylogeny, which has led to the erection of several new genera (Takayama, Akashiwo, Karenia, and Karlodinium). Taking the apical groove characteristics and molecular phylogeny combined approach, we reexamined the historically taxonomically uncertain species Cochlodinium geminatum that formed massive blooms in Pearl River Estuary, China, in recent years. Samples were collected from a bloom in 2011 for morphological, characteristic pigment, and molecular analyses. We found that the cingulum in this species wraps around the cell body about 1.2 turns on average but can appear under the light microscopy to be >1.5 turns after the cells have been preserved. The shape of its apical groove, however, was stably an open-ended anticlockwise loop of kidney bean shape, similar to that of Polykrikos. Furthermore, the molecular phylogenetic analysis using 18S rRNA-ITS-28S rRNA gene cistron we obtained in this study also consistently placed this species closest to Polykrikos within the Gymnodinium sensu stricto clade and set it far separated from the clade of Cochlodinium. These results suggest that this species should be transferred to Polykrikos as Polykrikos geminatum. Our results reiterate the need to use the combination of apical groove morphology and molecular phylogeny for the classification of species within the genus of Cochlodinium and other Gymnodiniales lineages.
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Affiliation(s)
- Dajun Qiu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China
- * E-mail: (DQ); (SL)
| | - Liangmin Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China
| | - Sheng Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Senjie Lin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
- * E-mail: (DQ); (SL)
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35
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Kosakyan A, Gomaa F, Mitchell EA, Heger TJ, Lara E. Using DNA-barcoding for sorting out protist species complexes: A case study of the Nebela tincta–collaris–bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae). Eur J Protistol 2013; 49:222-37. [DOI: 10.1016/j.ejop.2012.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/28/2022]
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Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea). Protist 2013; 164:24-36. [DOI: 10.1016/j.protis.2011.12.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/20/2011] [Accepted: 12/20/2011] [Indexed: 11/17/2022]
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Soehner S, Zinssmeister C, Kirsch M, Gottschling M. Who am I — and if so, how many? Species diversity of calcareous dinophytes (Thoracosphaeraceae, Peridiniales) in the Mediterranean Sea. ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0109-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Hoppenrath M, Murray S, Sparmann SF, Leander BS. MORPHOLOGY AND MOLECULAR PHYLOGENY OF ANKISTRODINIUM GEN. NOV. (DINOPHYCEAE), A NEW GENUS OF MARINE SAND-DWELLING DINOFLAGELLATES FORMERLY CLASSIFIED WITHIN AMPHIDINIUM(1). JOURNAL OF PHYCOLOGY 2012; 48:1143-1152. [PMID: 27011274 DOI: 10.1111/j.1529-8817.2012.01198.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The classical athecate dinoflagellate genera (Amphidinium, Gymnodinium, Gyrodinium) have long been recognized to be polyphyletic. Amphidinium sensu lato is the most diverse of all marine benthic dinoflagellate genera; however, following the redefinition of this genus ∼100 species remain now of uncertain or unknown generic affiliation. In an effort to improve our taxonomic and phylogenetic understanding of one of these species, namely Amphidinium semilunatum, we re-investigated organisms from several distant sites around the world using light and scanning electron microscopy and molecular phylogenetic methods. Our results enabled us to describe this species within a new heterotrophic genus, Ankistrodinium. Cells of A. semilunatum were strongly laterally flattened, rounded-quadrangular to oval in lateral view, and possessed a small asymmetrical epicone. The sulcus was wide and characteristically deeply incised on the hypocone running around the antapex and reaching the dorsal side. The straight acrobase with hook-shaped end started at the sulcal extension and continued onto the epicone. The molecular phylogenetic results clearly showed that A. semilunatum is a distinct taxon and is only distantly related to species within the genus Amphidinium sensu stricto. The nearest sister group to Ankistrodinium could not be reliably determined.
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Affiliation(s)
- Mona Hoppenrath
- Forschungsinstitut Senckenberg, Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany Departments of Zoology and Botany, University of British Columbia, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, BC V67 1Z4, CanadaSchool of Biotechnology and Biomolecular Sciences, University of NSW, Sydney NSW 2052, Australia The Sydney Institute of Marine Sciences, Chowder Bay Road, Mosman, NSW 2088 AustraliaDepartments of Zoology and Botany, University of British Columbia, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, BC V67 1Z4, Canada
| | - Shauna Murray
- Forschungsinstitut Senckenberg, Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany Departments of Zoology and Botany, University of British Columbia, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, BC V67 1Z4, CanadaSchool of Biotechnology and Biomolecular Sciences, University of NSW, Sydney NSW 2052, Australia The Sydney Institute of Marine Sciences, Chowder Bay Road, Mosman, NSW 2088 AustraliaDepartments of Zoology and Botany, University of British Columbia, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, BC V67 1Z4, Canada
| | - Sarah F Sparmann
- Forschungsinstitut Senckenberg, Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany Departments of Zoology and Botany, University of British Columbia, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, BC V67 1Z4, CanadaSchool of Biotechnology and Biomolecular Sciences, University of NSW, Sydney NSW 2052, Australia The Sydney Institute of Marine Sciences, Chowder Bay Road, Mosman, NSW 2088 AustraliaDepartments of Zoology and Botany, University of British Columbia, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, BC V67 1Z4, Canada
| | - Brian S Leander
- Forschungsinstitut Senckenberg, Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany Departments of Zoology and Botany, University of British Columbia, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, BC V67 1Z4, CanadaSchool of Biotechnology and Biomolecular Sciences, University of NSW, Sydney NSW 2052, Australia The Sydney Institute of Marine Sciences, Chowder Bay Road, Mosman, NSW 2088 AustraliaDepartments of Zoology and Botany, University of British Columbia, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, BC V67 1Z4, Canada
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Luddington IA, Kaczmarska I, Lovejoy C. Distance and character-based evaluation of the V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae). PLoS One 2012; 7:e45664. [PMID: 23029169 PMCID: PMC3448646 DOI: 10.1371/journal.pone.0045664] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Accepted: 08/21/2012] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is a molecular tool that exploits a unique DNA sequence of a standardized gene or non-coding region for the species identification of unknown individuals. The investigation into a suitable barcode for diatoms is ongoing and there are several promising candidates including mitochondrial, plastidial and nuclear markers. We analyzed 272 sequences from 76 diatoms species in the orders Thalassiosirales, Lithodesmiales and Cymatosirales, using distance and character based approaches, to assess the applicability of a DNA barcode based on the hypervariable V4 region of the nuclear 18S rRNA gene. We show that the proposed V4 barcode separated ca. 97% of all centric diatom taxa tested using a threshold p-distance of 0.02 and that many problem pairs were further separated using a character based approach. The reliability of amplification, extensive reference library and variability seen in the V4 region make it the most promising candidate to date for a barcode marker for diatoms particularly when combined with DNA character analysis.
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Affiliation(s)
- Ian A Luddington
- Department of Biology, Mount Allison University, Sackville, Canada.
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Stern RF, Andersen RA, Jameson I, Küpper FC, Coffroth MA, Vaulot D, Le Gall F, Véron B, Brand JJ, Skelton H, Kasai F, Lilly EL, Keeling PJ. Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker. PLoS One 2012; 7:e42780. [PMID: 22916158 PMCID: PMC3420951 DOI: 10.1371/journal.pone.0042780] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 07/12/2012] [Indexed: 11/19/2022] Open
Abstract
Background DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates. Methodology/Principal Findings The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name. Conclusions/Significance The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.
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Affiliation(s)
- Rowena F Stern
- The Laboratory, Sir Alister Hardy Foundation for Ocean Science, Plymouth, United Kingdom.
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Murray SA, Garby T, Hoppenrath M, Neilan BA. Genetic diversity, morphological uniformity and polyketide production in dinoflagellates (Amphidinium, Dinoflagellata). PLoS One 2012; 7:e38253. [PMID: 22675531 PMCID: PMC3366924 DOI: 10.1371/journal.pone.0038253] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 05/06/2012] [Indexed: 11/19/2022] Open
Abstract
Dinoflagellates are an intriguing group of eukaryotes, showing many unusual morphological and genetic features. Some groups of dinoflagellates are morphologically highly uniform, despite indications of genetic diversity. The species Amphidinium carterae is abundant and cosmopolitan in marine environments, grows easily in culture, and has therefore been used as a 'model' dinoflagellate in research into dinoflagellate genetics, polyketide production and photosynthesis. We have investigated the diversity of 'cryptic' species of Amphidinium that are morphologically similar to A. carterae, including the very similar species Amphidinium massartii, based on light and electron microscopy, two nuclear gene regions (LSU rDNA and ITS rDNA) and one mitochondrial gene region (cytochrome b). We found that six genetically distinct cryptic species (clades) exist within the species A. massartii and four within A. carterae, and that these clades differ from one another in molecular sequences at levels comparable to other dinoflagellate species, genera or even families. Using primers based on an alignment of alveolate ketosynthase sequences, we isolated partial ketosynthase genes from several Amphidinium species. We compared these genes to known dinoflagellate ketosynthase genes and investigated the evolution and diversity of the strains of Amphidinium that produce them.
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Affiliation(s)
- Shauna A Murray
- School of Biotechnology and Biomolecular Sciences and Evolution and Ecology Research Centre, University of New South Wales, New South Wales, Sydney, Australia.
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Kosakyan A, Heger TJ, Leander BS, Todorov M, Mitchell EA, Lara E. COI Barcoding of Nebelid Testate Amoebae (Amoebozoa: Arcellinida): Extensive Cryptic Diversity and Redefinition of the Hyalospheniidae Schultze. Protist 2012; 163:415-34. [DOI: 10.1016/j.protis.2011.10.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 09/17/2011] [Indexed: 11/30/2022]
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43
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Dilcher M, Hasib L, Lechner M, Wieseke N, Middendorf M, Marz M, Koch A, Spiegel M, Dobler G, Hufert FT, Weidmann M. Genetic characterization of Tribeč virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses. Virology 2012; 423:68-76. [DOI: 10.1016/j.virol.2011.11.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 09/17/2011] [Accepted: 11/17/2011] [Indexed: 11/24/2022]
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Anderson DM, Alpermann TJ, Cembella AD, Collos Y, Masseret E, Montresor M. The globally distributed genus Alexandrium: multifaceted roles in marine ecosystems and impacts on human health. HARMFUL ALGAE 2012; 14:10-35. [PMID: 22308102 PMCID: PMC3269821 DOI: 10.1016/j.hal.2011.10.012] [Citation(s) in RCA: 369] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The dinoflagellate genus Alexandrium is one of the major harmful algal bloom (HAB) genera with respect to the diversity, magnitude and consequences of blooms. The ability of Alexandrium to colonize multiple habitats and to persist over large regions through time is testimony to the adaptability and resilience of this group of species. Three different families of toxins, as well as an as yet incompletely characterized suite of allelochemicals are produced among Alexandrium species. Nutritional strategies are equally diverse, including the ability to utilize a range of inorganic and organic nutrient sources, and feeding by ingestion of other organisms. Many Alexandrium species have complex life histories that include sexuality and often, but not always, cyst formation, which is characteristic of a meroplanktonic life strategy and offers considerable ecological advantages. Due to the public health and ecosystem impacts of Alexandrium blooms, the genus has been extensively studied, and there exists a broad knowledge base that ranges from taxonomy and phylogeny through genomics and toxin biosynthesis to bloom dynamics and modeling. Here we present a review of the genus Alexandrium, focusing on the major toxic and otherwise harmful species.
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Affiliation(s)
- Donald M Anderson
- Woods Hole Oceanographic Institution, MS # 32, 266 Woods Hole Road, Woods Hole MA 02543; 508 289 2351
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Qiu D, Huang L, Liu S, Lin S. Nuclear, mitochondrial and plastid gene phylogenies of Dinophysis miles (Dinophyceae): evidence of variable types of chloroplasts. PLoS One 2011; 6:e29398. [PMID: 22242118 PMCID: PMC3248434 DOI: 10.1371/journal.pone.0029398] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 11/28/2011] [Indexed: 11/30/2022] Open
Abstract
The Dinophysis genus is an ecologically and evolutionarily important group of marine dinoflagellates, yet their molecular phylogenetic positions and ecological characteristics such as trophic modes remain poorly understood. Here, a population of Dinophysis miles var. indica was sampled from South China Sea in March 2010. Nuclear ribosomal RNA gene (rDNA) SSU, ITS1-5.8S-ITS2 and LSU, mitochondrial genes encoding cytochrome B (cob) and cytochrome C oxidase subunit I (cox1), and plastid rDNA SSU were PCR amplified and sequenced. Phylogenetic analyses based on cob, cox1, and the nuclear rRNA regions showed that D. miles was closely related to D. tripos and D. caudata while distinct from D. acuminata. Along with morphology the LSU and ITS1-5.8S-ITS2 molecular data confirmed that this population was D. miles var. indica. Furthermore, the result demonstrated that ITS1-5.8S-ITS2 fragment was the most effective region to distinguish D. miles from other Dinophysis species. Three distinct types of plastid rDNA sequences were detected, belonging to plastids of a cryptophyte, a haptophyte, and a cyanobacterium, respectively. This is the first documentation of three photosynthetic entities associated with a Dinophysis species. While the cyanobacterial sequence likely represented an ectosymbiont of the D. miles cells, the detection of the cryptophyte and haptophyte plastid sequences indicates that the natural assemblage of D. miles likely retain more than one type of plastids from its prey algae for temporary use in photosynthesis. The result, together with recent findings of plastid types in other Dinophysis species, suggests that more systematic research is required to understand the complex nutritional physiology of this genus of dinoflagellates.
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Affiliation(s)
- Dajun Qiu
- Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Liangmin Huang
- Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China
| | - Sheng Liu
- Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, China
| | - Senjie Lin
- Key Laboratory of Marine Bio-resources Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
- * E-mail:
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Murray SA, Wiese M, Stüken A, Brett S, Kellmann R, Hallegraeff G, Neilan BA. sxtA-based quantitative molecular assay to identify saxitoxin-producing harmful algal blooms in marine waters. Appl Environ Microbiol 2011; 77:7050-7. [PMID: 21841034 PMCID: PMC3187097 DOI: 10.1128/aem.05308-11] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 07/29/2011] [Indexed: 11/20/2022] Open
Abstract
The recent identification of genes involved in the production of the potent neurotoxin and keystone metabolite saxitoxin (STX) in marine eukaryotic phytoplankton has allowed us for the first time to develop molecular genetic methods to investigate the chemical ecology of harmful algal blooms in situ. We present a novel method for detecting and quantifying the potential for STX production in marine environmental samples. Our assay detects a domain of the gene sxtA that encodes a unique enzyme putatively involved in the sxt pathway in marine dinoflagellates, sxtA4. A product of the correct size was recovered from nine strains of four species of STX-producing Alexandrium and Gymnodinium catenatum and was not detected in the non-STX-producing Alexandrium species, other dinoflagellate cultures, or an environmental sample that did not contain known STX-producing species. However, sxtA4 was also detected in the non-STX-producing strain of Alexandrium tamarense, Tasmanian ribotype. We investigated the copy number of sxtA4 in three strains of Alexandrium catenella and found it to be relatively constant among strains. Using our novel method, we detected and quantified sxtA4 in three environmental blooms of Alexandrium catenella that led to STX uptake in oysters. We conclude that this method shows promise as an accurate, fast, and cost-effective means of quantifying the potential for STX production in marine samples and will be useful for biological oceanographic research and harmful algal bloom monitoring.
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Affiliation(s)
- Shauna A Murray
- Sydney Institute of Marine Sciences, Chowder Bay Road, Mosman, NSW 2088, Australia.
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Lin S. Genomic understanding of dinoflagellates. Res Microbiol 2011; 162:551-69. [PMID: 21514379 DOI: 10.1016/j.resmic.2011.04.006] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 03/02/2011] [Indexed: 10/18/2022]
Abstract
The phylum of dinoflagellates is characterized by many unusual and interesting genomic and physiological features, the imprint of which, in its immense genome, remains elusive. Much novel understanding has been achieved in the last decade on various aspects of dinoflagellate biology, but most remarkably about the structure, expression pattern and epigenetic modification of protein-coding genes in the nuclear and organellar genomes. Major findings include: 1) the great diversity of dinoflagellates, especially at the base of the dinoflagellate tree of life; 2) mini-circularization of the genomes of typical dinoflagellate plastids (with three membranes, chlorophylls a, c1 and c2, and carotenoid peridinin), the scrambled mitochondrial genome and the extensive mRNA editing occurring in both systems; 3) ubiquitous spliced leader trans-splicing of nuclear-encoded mRNA and demonstrated potential as a novel tool for studying dinoflagellate transcriptomes in mixed cultures and natural assemblages; 4) existence and expression of histones and other nucleosomal proteins; 5) a ribosomal protein set expected of typical eukaryotes; 6) genetic potential of non-photosynthetic solar energy utilization via proton-pump rhodopsin; 7) gene candidates in the toxin synthesis pathways; and 8) evidence of a highly redundant, high gene number and highly recombined genome. Despite this progress, much more work awaits genome-wide transcriptome and whole genome sequencing in order to unfold the molecular mechanisms underlying the numerous mysterious attributes of dinoflagellates.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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48
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Stern RF, Horak A, Andrew RL, Coffroth MA, Andersen RA, Küpper FC, Jameson I, Hoppenrath M, Véron B, Kasai F, Brand J, James ER, Keeling PJ. Environmental barcoding reveals massive dinoflagellate diversity in marine environments. PLoS One 2010; 5:e13991. [PMID: 21085582 PMCID: PMC2981561 DOI: 10.1371/journal.pone.0013991] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Accepted: 10/12/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments. METHODOLOGY/PRINCIPAL FINDINGS In this study, we assembled a large cytochrome c oxidase 1 (COI) barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean), including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species. CONCLUSIONS/SIGNIFICANCE COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights the extent to which we underestimate microbial diversity in the environment.
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Affiliation(s)
- Rowena F Stern
- The Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
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Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates. Proc Natl Acad Sci U S A 2010; 107:20033-8. [PMID: 21041634 DOI: 10.1073/pnas.1007246107] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Environmental transcriptomics (metatranscriptomics) for a specific lineage of eukaryotic microbes (e.g., Dinoflagellata) would be instrumental for unraveling the genetic mechanisms by which these microbes respond to the natural environment, but it has not been exploited because of technical difficulties. Using the recently discovered dinoflagellate mRNA-specific spliced leader as a selective primer, we constructed cDNA libraries (e-cDNAs) from one marine and two freshwater plankton assemblages. Small-scale sequencing of the e-cDNAs revealed functionally diverse transcriptomes proven to be of dinoflagellate origin. A set of dinoflagellate common genes and transcripts of dominant dinoflagellate species were identified. Further analyses of the dataset prompted us to delve into the existing, largely unannotated dinoflagellate EST datasets (DinoEST). Consequently, all four nucleosome core histones, two histone modification proteins, and a nucleosome assembly protein were detected, clearly indicating the presence of nucleosome-like machinery long thought not to exist in dinoflagellates. The isolation of rhodopsin from taxonomically and ecotypically diverse dinoflagellates and its structural similarity and phylogenetic affinity to xanthorhodopsin suggest a common genetic potential in dinoflagellates to use solar energy nonphotosynthetically. Furthermore, we found 55 cytoplasmic ribosomal proteins (RPs) from the e-cDNAs and 24 more from DinoEST, showing that the dinoflagellate phylum possesses all 79 eukaryotic RPs. Our results suggest that a sophisticated eukaryotic molecular machine operates in dinoflagellates that likely encodes many more unsuspected physiological capabilities and, meanwhile, demonstrate that unique spliced leaders are useful for profiling lineage-specific microbial transcriptomes in situ.
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50
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Lowe CD, Montagnes DJ, Martin LE, Watts PC. Patterns of Genetic Diversity in the Marine Heterotrophic Flagellate Oxyrrhis marina (Alveolata: Dinophyceae). Protist 2010; 161:212-21. [DOI: 10.1016/j.protis.2009.11.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 08/01/2009] [Indexed: 11/28/2022]
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