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Lim YK, Park BS, Kim JH, Baek SS, Baek SH. Effect of marine heatwaves on bloom formation of the harmful dinoflagellate Cochlodinium polykrikoides: Two sides of the same coin? HARMFUL ALGAE 2021; 104:102029. [PMID: 34023074 DOI: 10.1016/j.hal.2021.102029] [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: 04/20/2020] [Revised: 02/01/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
In 2018, the bloom of harmful dinoflagellate Cochlodinium polykrikoides occurred under abnormally high water temperature (WT) conditions caused by heatwaves in Korean coastal water (KCW). To better understand C. polykrikoides bloom at high WTs in 2018, we conducted field survey and laboratory experiments (the physiological and genetic differences between the two strains, CP2013 and CP2018). The heatwave increased the WT from 24.1°C to 29.2°C for two weeks, leading to strong stratification even in mid July (p < 0.01, Chi square = 94.656, Kruskal-Wallis test). Under early stratification conditions, patch blooms formed more earlier than the average outbreak in the last 17 years in KCW, despite high WT reaching 30°C. In laboratory experiments, although there were no genetic differences in the LSU rDNA, both strains showed a significant different growth response to high WTs; above 28°C, CP2013 did not survive, but CP2018 was able to grow, suggesting that CP2018 had potential growth capacity at high WTs. However, the growth rate and yield of the culture (CP2018) were lowered at 30°C. Also, the blooms of C. polykrikoides in 2018 lasted only 3 weeks, which is unusual short compared to the average duration since 2002. The negative correlation between the average WT and duration of C. polykrikoides bloom in previous 17 years (R2 = 0.518, p < 0.01) supports that high WT approaching 30°C is not favorable for C. polykrikoides in KCW. Thus, our findings indicated that in relation to heatwaves, early stratification condition plays a critical role in developing C. polykrikoides blooms, but maintaining bloom are negatively affected under high WT conditions.
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Affiliation(s)
- Young Kyun Lim
- Risk Assessment Research Center, KIOST (Korea Institute of Ocean Science and Technology), Geoje 53201, Korea; Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Bum Soo Park
- Marine Ecosystem Research Center, KIOST (Korea Institute of Ocean Science and Technology), Busan, 49111, Republic of Korea
| | - Jin Ho Kim
- Risk Assessment Research Center, KIOST (Korea Institute of Ocean Science and Technology), Geoje 53201, Korea; DNA Analysis Division, National Forensic Service, Seoul, 08036, Republic of Korea
| | - Sang-Soo Baek
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Seung Ho Baek
- Risk Assessment Research Center, KIOST (Korea Institute of Ocean Science and Technology), Geoje 53201, Korea; Department of Ocean Science, University of Science and Technology, Daejeon 34113, Republic of Korea.
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2
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Yarimizu K, Sildever S, Hamamoto Y, Tazawa S, Oikawa H, Yamaguchi H, Basti L, Mardones JI, Paredes-Mella J, Nagai S. Development of an absolute quantification method for ribosomal RNA gene copy numbers per eukaryotic single cell by digital PCR. HARMFUL ALGAE 2021; 103:102008. [PMID: 33980448 DOI: 10.1016/j.hal.2021.102008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
Recent increase of Harmful Algal Blooms (HAB) causes world-wide ecological, economical, and health issues, and more attention is paid to frequent coastal monitoring for the early detection of HAB species to prevent or reduce such impacts. Use of molecular tools in addition to traditional microscopy-based observation has become one of the promising methodologies for coastal monitoring. However, as ribosomal RNA (rRNA) genes are commonly targeted in molecular studies, variability in the rRNA gene copy number within and between species must be considered to provide quantitative information in quantitative PCR (qPCR), digital PCR (dPCR), and metabarcoding analyses. Currently, this information is only available for a limited number of species. The present study utilized a dPCR technology to quantify copy numbers of rRNA genes per single cell in 16 phytoplankton species, the majority of which are toxin-producers, using a newly developed universal primer set accompanied by a labeled probe with a fluorophore and a double-quencher. In silico PCR using the newly developed primers allowed the detection of taxa from 8 supergroups, demonstrating universality and broad coverage of the primer set. Chelex buffer was found to be suitable for DNA extraction to obtain DNA fragments with suitable size to avoid underestimation of the copy numbers. The study successfully demonstrated the first comparison of absolute quantification of 18S rRNA copy numbers per cell from 16 phytoplankton species by the dPCR technology.
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Affiliation(s)
- Kyoko Yarimizu
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan; Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, 1-3-2 22 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-8511, Japan
| | - Sirje Sildever
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan; Department of Marine Systems, Tallinn University of Technology, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Yoko Hamamoto
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Satoshi Tazawa
- AXIOHELIX Co. Ltd, 12-17 Kandaizumicho, Chiyoda-ku, Tokyo 101-0024, Japan
| | - Hiroshi Oikawa
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Haruo Yamaguchi
- Faculty of Agriculture and Marine Sciences, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Leila Basti
- Department of Ocean Sciences, Tokyo University of Marine Science and Technology, Minato, Tokyo 108-8477, Japan
| | - Jorge I Mardones
- Instituto de Fomento Pesquero, Centro de Estudios de Algas Nocivas (IFOP-CREAN), Padre Harter 574, Puerto Montt 5501679, Chile; Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Javier Paredes-Mella
- Instituto de Fomento Pesquero, Centro de Estudios de Algas Nocivas (IFOP-CREAN), Padre Harter 574, Puerto Montt 5501679, Chile
| | - Satoshi Nagai
- Japan Fisheries Research and Education Agency, Fisheries Resources Institute, Fisheries Stock Assessment Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan.
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3
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Potential Cause of Decrease in Bloom Events of the Harmful Dinoflagellate Cochlodinium polykrikoides in Southern Korean Coastal Waters in 2016. Toxins (Basel) 2020; 12:toxins12060390. [PMID: 32545486 PMCID: PMC7374724 DOI: 10.3390/toxins12060390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 11/17/2022] Open
Abstract
Blooms of the ichthyotoxic dinoflagellate Cochlodinium polykrikoides are responsible for massive fish mortality events in Korean coastal waters (KCW). They have been consistently present in southern KCW over the last two decades, but they were not observed in 2016, unlike in the previous years. Despite extensive studies, the cause of this absence of this dinoflagellate bloom remains largely unknown. Thus, we compared physico-chemical and biological data from along the Tongyeong coast between 2016 and the previous four years (2012–2015). The averages of water temperature and salinity in August, 2016 were significantly (p < 0.001) different from those in the previous years. The amount of Changjiang River discharge, which can affect the environmental conditions in the southern Korean coastal area via ocean currents, was larger than in the previous years, resulting in a reduction in the salinity level in August when blooms of C. polykrikoides usually occurred. Moreover, compared to previous years, in 2016, there was a weak expansion of C. polykrikoides blooms in the Goheung-Oenarodo area where C. polykrikoides blooms were annually initiated in KCW. Lastly, the strong winds from the typhoon Lionrock may also have contributed to the early termination of this dinoflagellate bloom. Together with these findings, the combination of these environmental conditions in 2016, unlike in previous years, may have inhibited the formation of C. polykrikoides blooms along the Tongyeong coast.
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Gao Y, Sassenhagen I, Richlen ML, Anderson DM, Martin JL, Erdner DL. Spatiotemporal genetic structure of regional-scale Alexandrium catenella dinoflagellate blooms explained by extensive dispersal and environmental selection. HARMFUL ALGAE 2019; 86:46-54. [PMID: 31358276 PMCID: PMC6668924 DOI: 10.1016/j.hal.2019.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 05/15/2023]
Abstract
Paralytic Shellfish Poisoning (PSP) caused by the dinoflagellate Alexandrium catenella is a well-known global syndrome that negatively impacts human health and fishery economies. Understanding the population dynamics and ecology of this species is thus important for identifying determinants of blooms and associated PSP toxicity. Given reports of extensive genetic heterogeneity in the toxicity and physiology of Alexandrium species, knowledge of genetic population structure in harmful algal species such as A. catenella can also facilitate the understanding of toxic bloom development and ecological adaptation. In this study we employed microsatellite markers to analyze multiple A. catenella strains isolated from several sub-regions in the Gulf of Maine (GoM) during summer blooms, to gain insights into the sources and dynamics of this economically important phytoplankton species. At least three genetically distinct clusters of A. catenella were identified in the GoM. Each cluster contained representatives from different sub-regions, highlighting the extent of connectivity and dispersal throughout the region. This shared diversity could result from cyst beds created by previous coastal blooms, thereby preserving the overall diversity of the regional A. catenella population. Rapid spatiotemporal genetic differentiation of A. catenella populations was observed in local blooms, likely driven by natural selection through environmental conditions such as silicate and nitrate/nitrite concentrations, emphasizing the role of short-term water mass intrusions and biotic processes in determining the diversity and dynamics of marine phytoplankton populations. Given the wide-spread intraspecific diversity of A. catenella in GoM and potentially elsewhere, harmful algal blooms will likely persist in many regions despite global warming and changing environmental conditions in the future. Selection of different genetic lineages through variable hydrological conditions might impact toxin production and profiles of future blooms, challenging HAB control and prediction of PSP risk in the future.
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Affiliation(s)
- Yida Gao
- Marine Science Institute, University of Texas at Austin, Port Aransas, TX, 78373, USA
| | - Ingrid Sassenhagen
- Marine Science Institute, University of Texas at Austin, Port Aransas, TX, 78373, USA; Laboratoire d'Océanologie et des Geosciences, UMR LOG 8187, Université du Littoral Côte d'Opale, Wimereux, France
| | - Mindy L Richlen
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | | | - Jennifer L Martin
- Fisheries and Oceans Canada, Biological Station, St. Andrews, NB, E5B 0E4, Canada
| | - Deana L Erdner
- Marine Science Institute, University of Texas at Austin, Port Aransas, TX, 78373, USA.
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Sildever S, Jerney J, Kremp A, Oikawa H, Sakamoto S, Yamaguchi M, Baba K, Mori A, Fukui T, Nonomura T, Shinada A, Kuroda H, Kanno N, Mackenzie L, Anderson DM, Nagai S. Genetic relatedness of a new Japanese isolates of Alexandrium ostenfeldii bloom population with global isolates. HARMFUL ALGAE 2019; 84:64-74. [PMID: 31128814 PMCID: PMC6540814 DOI: 10.1016/j.hal.2019.02.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/12/2019] [Accepted: 02/02/2019] [Indexed: 05/13/2023]
Abstract
In recent years, blooms of toxic Alexandrium ostenfeldii strains have been reported from around the world. In 2013, the species formed a red tide in a shallow lagoon in western Japan, which was the first report of the species in the area. To investigate the genetic relatedness of Japanese A. ostenfeldii and global isolates, the full-length SSU, ITS and LSU sequences were determined, and phylogenetic analyses were conducted for isolates from western and northern Japan and from the Baltic Sea. Genotyping and microsatellite sequence comparison were performed to estimate the divergence and connectivity between the populations from western Japan and the Baltic Sea. In all phylogenetic analyses, the isolates from western Japan grouped together with global isolates from shallow and low saline areas, such as the Baltic Sea, estuaries on the east coast of U.S.A. and from the Bohai Sea, China. In contrast, the isolates from northern Japan formed a well-supported separate group in the ITS and LSU phylogenies, indicating differentiation between the Japanese populations. This was further supported by the notable differentiation between the sequences of western and northern Japanese isolates, whereas the lowest differentiation was found between the western Japanese and Chinese isolates. Microsatellite genotyping revealed low genetic diversity in the western Japanese population, possibly explained by a recent introduction to the lagoon from where it was detected. The red tide recorded in the shallow lagoon followed notable changes in the salinity of the waterbody and phytoplankton composition, potentially facilitating the bloom of A. ostenfeldii.
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Affiliation(s)
- Sirje Sildever
- National Research Institute of Fisheries Science, Yokohama, Kanagawa, 236-8648, Japan
| | - Jacqueline Jerney
- Finnish Environment Institute, Marine Research Centre, Agnes Sjöberginkatu 2, 00790 Helsinki, Finland
| | - Anke Kremp
- Finnish Environment Institute, Marine Research Centre, Agnes Sjöberginkatu 2, 00790 Helsinki, Finland
| | - Hiroshi Oikawa
- National Research Institute of Fisheries Science, Yokohama, Kanagawa, 236-8648, Japan
| | - Setsuko Sakamoto
- National Research Institute of Fisheries and Environment of Inland Sea, Hatsukaichi, Hiroshima, 739-0452, Japan
| | | | - Katsuhisa Baba
- Hokkaido Research Organization, Fisheries Research Department, Central Fisheries Research Institute, Yoichi, Hokkaido, 046-855, Japan
| | - Akihiro Mori
- Tottori Prefecture Water Environment Management Division, 1-220 Higashimachi, Tottori 680-8570, Japan
| | - Toshinori Fukui
- Tottori Prefectural Fisheries Research Center, 1166 Ishiwaki, Yurihama-cho, Tohaku-gun, Tottori Prefecture, 689-0602, Japan
| | - Takumi Nonomura
- Tottori Prefectural Fisheries Research Center, 1166 Ishiwaki, Yurihama-cho, Tohaku-gun, Tottori Prefecture, 689-0602, Japan
| | - Akiyoshi Shinada
- Central Fisheries Research Institute, 238 Hamanaka, Yoichi, Hokkaido, 046-8555, Japan
| | - Hiroshi Kuroda
- Hokkaido National Fisheries Research Institute, 116 Katsurakoi, Kushiro, Hokkaido, 085-0802, Japan
| | - Nanako Kanno
- National Research Institute of Fisheries Science, Yokohama, Kanagawa, 236-8648, Japan
| | - Lincoln Mackenzie
- Cawthron Institute, 98 Halifax Street East, Nelson 7010, New Zealand
| | - Donald M Anderson
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02543-1050 USA
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Yokohama, Kanagawa, 236-8648, Japan.
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Thoha H, Muawanah, Bayu Intan MD, Rachman A, Sianturi OR, Sidabutar T, Iwataki M, Takahashi K, Avarre JC, Masseret E. Resting Cyst Distribution and Molecular Identification of the Harmful Dinoflagellate Margalefidinium polykrikoides (Gymnodiniales, Dinophyceae) in Lampung Bay, Sumatra, Indonesia. Front Microbiol 2019; 10:306. [PMID: 30846977 PMCID: PMC6393338 DOI: 10.3389/fmicb.2019.00306] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Abstract
Margalefidinium polykrikoides, an unarmored dinoflagellate, was suspected to be the causative agent of the harmful algal blooms - associated with massive fish mortalities - that have occurred continually in Lampung Bay, Indonesia, since the first bloom event in October 2012. In this study, after examination of the morphology of putative M. polykrikoides-like cysts sampled in bottom sediments, cyst bed distribution of this harmful species was explored in the inner bay. Sediment samples showed that resting cysts, including several morphotypes previously reported as M. polykrikoides, were most abundant on the northern coast of Lampung Bay, ranging from 20.6 to 645.6 cysts g-1 dry sediment. Molecular phylogeny inferred from LSU rDNA revealed that the so-called Mediterranean ribotype was detected in the sediment while M. polykrikoides motile cells, four-cell chain forming in bloom conditions, belonged to the American-Malaysian ribotype. Moreover, hyaline cysts, exclusively in the form of four-cell chains, were also recorded. Overall, these results unequivocally show that the species M. polykrikoides is abundantly present, in the form of vegetative cells, hyaline and resting cysts in an Indonesian area.
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Affiliation(s)
- Hikmah Thoha
- Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta, Indonesia
| | - Muawanah
- Main Center for Marine Aquaculture of Lampung, Directorate General of Aquaculture, Lampung, Indonesia
| | - Mariana D. Bayu Intan
- Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta, Indonesia
| | - Arief Rachman
- Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta, Indonesia
| | - Oksto Ridho Sianturi
- Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta, Indonesia
| | - Tumpak Sidabutar
- Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta, Indonesia
| | - Mitsunori Iwataki
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
| | - Kazuya Takahashi
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
| | | | - Estelle Masseret
- Research Center for Oceanography, Indonesian Institute of Sciences, Jakarta, Indonesia
- MARBEC, University of Montpellier, IRD, Ifremer, CNRS, Montpellier, France
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Sundqvist L, Godhe A, Jonsson PR, Sefbom J. The anchoring effect-long-term dormancy and genetic population structure. ISME JOURNAL 2018; 12:2929-2941. [PMID: 30068937 DOI: 10.1038/s41396-018-0216-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 05/18/2018] [Accepted: 06/11/2018] [Indexed: 11/09/2022]
Abstract
Understanding the genetic structure of populations is key to revealing past and present demographic and evolutionary processes in a species. In the past decade high genetic differentiation has been observed in many microbial species challenging the previous view of cosmopolitan distribution. Populations have displayed high genetic differentiation, even at small spatial scales, despite apparent high dispersal. Numerous species of microalgae have a life-history strategy that includes a long-term resting stage, which can accumulate in sediments and serve as refuge during adverse conditions. It is presently unclear how these seed banks affect the genetic structure of populations in aquatic environments. Here we provide a conceptual framework, using a simple model, to show that long-term resting stages have an anchoring effect on populations leading to increased genetic diversity and population differentiation in the presence of gene flow. The outcome that species with resting stages have a higher degree of genetic differentiation compared to species without, is supported by empirical data obtained from a systematic literature review. With this work we propose that seed banks in aquatic microalgae play an important role in the contradicting patterns of gene flow, and ultimately the adaptive potential and population dynamics in species with long-term resting stages.
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Affiliation(s)
- Lisa Sundqvist
- Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE, 40530, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE, 40530, Sweden
| | - Per R Jonsson
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Strömstad, SE, 45296, Sweden
| | - Josefin Sefbom
- Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE, 40530, Sweden. .,Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, Gent, B-9000, Belgium.
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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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9
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Dzhembekova N, Urusizaki S, Moncheva S, Ivanova P, Nagai S. Applicability of massively parallel sequencing on monitoring harmful algae at Varna Bay in the Black Sea. HARMFUL ALGAE 2017; 68:40-51. [PMID: 28962989 DOI: 10.1016/j.hal.2017.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/04/2017] [Accepted: 07/17/2017] [Indexed: 06/07/2023]
Abstract
In this study the plankton diversity in 13 environmental samples from Varna Bay (in the western Black Sea) was analyzed using massively parallel sequencing (MPS). This preliminary study was undertaken to assess the potential of this technology for future implementation in monitoring programs in the Black Sea. Amplicon sequences of the 18S rRNA gene (V4-5 regions) were obtained using the Illumina MiSeq 250PE platform. A total of 1137 operational taxonomic units (OTUs) were obtained among which 242 OTUs with >0.990 BLAST top hit similarity (21.3% of all detected OTUs) closely related to sequences belonging to -protists. A large portion (175 OTUs=72.3%) was identified at the species levels, including species typical for the Bulgarian Black Sea plankton community, as well as many that haven't been reported earlier in the Bulgarian Black Sea coast (124 OTUs=51.2%). Dinoflagellates were represented by the highest species number (77 OTUs comprising 31.8% of protist species), with dominant genera Gyrodinium and Heterocapsa. The present survey revealed the presence of 12 species listed as harmful, some of which have been previously overlooked, such as Cochlodinium polykrikoides, Karenia bicuneiformis, and Karlodinium veneficum. Species identification was possible for 10.3-36.0% of the detected OTUs in the six major supergroups. The frequency in Rhizaria was significantly lower than that in other major groups (p<0.05-0.01), implying difficulties in the classification from morphology-based observations. The metagenetic data had an insufficient resolution of the 18S rRNA gene for species identification in many genera. These issues may hamper the implementation of MPS-based surveys for plankton monitoring, especially for detecting harmful algal blooms (HAB). The sequencing technology is steadily improving and it is expected that sequence length and quality issues will be resolved in the near future. The ongoing efforts to register taxonomic information and quality controls in the international nucleotide sequence databases (INSDs) will be essential for improving taxonomic identification power.
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Affiliation(s)
- Nina Dzhembekova
- Institute of Oceanology, Bulgarian Academy of Sciences, First May street 40, 152, Varna 9000, Bulgaria
| | - Shingo Urusizaki
- AXIOHELIX Co. Ltd., 5-11 Hakozaki, Nihonbashi, Chuouku 103-0015, Tokyo, Japan
| | - Snejana Moncheva
- Institute of Oceanology, Bulgarian Academy of Sciences, First May street 40, 152, Varna 9000, Bulgaria
| | - Petya Ivanova
- Institute of Oceanology, Bulgarian Academy of Sciences, First May street 40, 152, Varna 9000, Bulgaria
| | - Satoshi Nagai
- Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan.
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10
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Higashi A, Nagai S, Seoane S, Ueki S. A hypervariable mitochondrial protein coding sequence associated with geographical origin in a cosmopolitan bloom-forming alga, Heterosigma akashiwo. Biol Lett 2017; 13:rsbl.2016.0976. [PMID: 28404821 DOI: 10.1098/rsbl.2016.0976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/21/2017] [Indexed: 11/12/2022] Open
Abstract
Geographical distributions of phytoplankton species can be defined by events on both evolutionary time and shorter scales, e.g. recent climate changes. Additionally, modern industrial activity, including the transport of live fish and spat for aquaculture and aquatic microorganisms in ship ballast water, may aid the spread of phytoplankton. Obtaining a reliable marker is key to gaining insight into the phylogeographic history of a species. Here, we report a hypervariable mitochondrial gene in the cosmopolitan bloom-forming alga, Heterosigma akashiwo We compared the entire mitochondrial genome sequences of seven H. akashiwo strains from Japanese and North American coastal waters and identified a hypervariable segment. The region codes for a hypothetical protein with no defined function, and its variations between Japanese and North American isolates were prominent, while the sequences were more conserved among Japanese strains and North American isolates. Comparison of the sequence in isolates obtained from different geographical points in the Northern Hemisphere revealed that the sequence variations largely correlated with latitude and longitude (i.e. Pacific/Atlantic oceans). Our results demonstrate the usefulness of the sequence in determining the phylogeographic history of H. akashiwo.
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Affiliation(s)
- Aiko Higashi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Sergio Seoane
- Department of Plant Biology and Ecology, University of the Basque Country, 48940 Leioa, Spain
| | - Shoko Ueki
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama 710-0046, Japan
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11
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Lundholm N, Ribeiro S, Godhe A, Rostgaard Nielsen L, Ellegaard M. Exploring the impact of multidecadal environmental changes on the population genetic structure of a marine primary producer. Ecol Evol 2017; 7:3132-3142. [PMID: 28480012 PMCID: PMC5415532 DOI: 10.1002/ece3.2906] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/13/2017] [Accepted: 02/21/2017] [Indexed: 01/29/2023] Open
Abstract
Many marine protists form resting stages that can remain viable in coastal sediments for several decades. Their long‐term survival offers the possibility to explore the impact of changes in environmental conditions on population dynamics over multidecadal time scales. Resting stages of the phototrophic dinoflagellate Pentapharsodinium dalei were isolated and germinated from five layers in dated sediment cores from Koljö fjord, Sweden, spanning ca. 1910–2006. This fjord has, during the last century, experienced environmental fluctuations linked to hydrographic variability mainly driven by the North Atlantic Oscillation. Population genetic analyses based on six microsatellite markers revealed high genetic diversity and suggested that samples belonged to two clusters of subpopulations that have persisted for nearly a century. We observed subpopulation shifts coinciding with changes in hydrographic conditions. The large degree of genetic diversity and the potential for both fluctuation and recovery over longer time scales documented here, may help to explain the long‐term success of aquatic protists that form resting stages.
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Affiliation(s)
- Nina Lundholm
- The Natural History Museum of Denmark University of Copenhagen Copenhagen K Denmark
| | - Sofia Ribeiro
- Glaciology and Climate Department Geological Survey of Denmark and Greenland (GEUS) Copenhagen K Denmark
| | - Anna Godhe
- Department of Marine Sciences University of Gothenburg Göteborg Sweden
| | - Lene Rostgaard Nielsen
- Deparment of Geosciences and Natural Resource Management University of Copenhagen Frederiksberg Denmark
| | - Marianne Ellegaard
- Department of Plant and Environmental Sciences University of Copenhagen Frederiksberg Denmark
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12
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Genetic Variations of the Parasitic Dinoflagellate Hematodinium Infecting Cultured Marine Crustaceans in China. Protist 2016; 167:597-609. [DOI: 10.1016/j.protis.2016.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/09/2016] [Accepted: 10/08/2016] [Indexed: 12/24/2022]
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13
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Park TG, Kim JJ, Kim WJ, Won KM. Development of real-time RT-PCR for detecting viable Cochlodinium polykrikoides (Dinophyceae) cysts in sediment. HARMFUL ALGAE 2016; 60:36-44. [PMID: 28073561 DOI: 10.1016/j.hal.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 09/09/2016] [Accepted: 10/22/2016] [Indexed: 06/06/2023]
Abstract
Morphological observations have confirmed that cysts are produced by dinoflagellates. However, finding a seed bed or unknown cysts in field samples by microscopy is extremely time consuming. Real-time PCR has been used to facilitate the detection of dinoflagellate cysts in sediment. However, DNA from dead vegetative cells remaining on the surface sediment may persist for a long period of time, which can cause false positive DNA detection. In this study, a non-quantitative RNA targeted probe using real-time RT-PCR was developed for detection of viable cysts in sediment. Large-subunit rRNA was used to develop a species-specific RNA targeted probe for the ichthyotoxic dinoflagellate Cochlodinium polykrikoides. The sediment samples were sieved and incubated at 30°C for 3h prior to RNA extraction to remove RNA from dead cells remaining in the sediment. Nested-PCR was conducted to maximize assay sensitivity. A field survey to determine the distribution of cysts at 155 sampling stations in the western and southern part of the Korean peninsula showed that C. polykrikoides cysts were detected at five sampling stations.
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Affiliation(s)
- Tae Gyu Park
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Tongyeong 650-943, Republic of Korea.
| | - Jin Joo Kim
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Tongyeong 650-943, Republic of Korea
| | - Won Jin Kim
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Tongyeong 650-943, Republic of Korea
| | - Kyoung Mi Won
- Southeast Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Tongyeong 650-943, Republic of Korea
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14
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Li Y, Huang HJ, Li H, Liu J, Yang W. Genetic diversity of Ulva prolifera population in Qingdao coastal water during the green algal blooms revealed by microsatellite. MARINE POLLUTION BULLETIN 2016; 111:237-246. [PMID: 27412412 DOI: 10.1016/j.marpolbul.2016.07.001] [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: 03/03/2016] [Revised: 06/30/2016] [Accepted: 07/01/2016] [Indexed: 06/06/2023]
Abstract
Green tides have occurred in Qingdao coast in China for seven consecutive years from 2007 to 2013. To provide information on the genetic structure of these blooms, 210 free-floating green algae samples isolated from the green tide in Qingdao coast on June 19, 2013 were identified based on the ITS, rbcL and 5S sequence, and genetic diversity was investigated by microsatellite markers. According to ITS, rbcL and 5S sequence, all the 210 samples belonged to Ulva prolifera. Nei's genetic diversity and Shannon index estimated using eight microsatellite markers indicated that the genetic diversity of U. prolifera population within Qingdao's green bloom in 2013 was low. Taking into account previous reports about life history and physiology of U. prolifera, we proposed that the limited origin area of the free-floating biomass and asexual reproduction of U. prolifera might be responsible for the lower diversity of free floating U. prolifera.
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Affiliation(s)
- Yue Li
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Hong-Jia Huang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Hongye Li
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Jiesheng Liu
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Weidong Yang
- Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China.
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15
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Nagai S, Miyamoto S, Ino K, Tajimi S, Nishi H, Tomono J. Easy detection of multiple Alexandrium species using DNA chromatography chip. HARMFUL ALGAE 2016; 51:97-106. [PMID: 28003065 DOI: 10.1016/j.hal.2015.10.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 10/17/2015] [Accepted: 10/24/2015] [Indexed: 06/06/2023]
Abstract
In this study, the Kaneka DNA chromatography chip (KDCC) for the Alexandrium species was successfully developed for simultaneous detection of five Alexandrium species. This method utilizes a DNA-DNA hybridization technology. In the PCR process, specifically designed tagged-primers are used, i.e. a forward primer consisting of a tag domain, which can conjugate with gold nanocolloids on the chip, and a primer domain, which can anneal/amplify the target sequence. However, the reverse primer consists of a tag domain, which can hybridize to the solid-phased capture probe on the chip, and a primer domain, which can anneal/amplify the target sequence. As a result, a red line that originates from gold nanocolloids appears as a positive signal on the chip, and the amplicon is detected visually by the naked eye. This technique is simple, because it is possible to visually detect the target species soon after (<5min) the application of 2μL of PCR amplicon and 65μL of development buffer to the sample pad of the chip. Further, this technique is relatively inexpensive and does not require expensive laboratory equipment, such as real-time Q-PCR machines or DNA microarray detectors, but a thermal cycler. Regarding the detection limit of KDCC for the five Alexandrium species, it varied among species and it was <0.1-10pg and equivalent to 5-500 copies of rRNA genes, indicating that the technique is sensitive enough for practical use to detect several cells of the target species from 1L of seawater. The detection sensitivity of KDCC was also evaluated with two different techniques, i.e. a multiplex-PCR and a digital DNA hybridization by digital DNA chip analyzer (DDCA), using natural plankton assemblages. There was no significant difference in the detection sensitivity among the three techniques, suggesting KDCC can be readily used to monitor the HAB species.
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Affiliation(s)
- Satoshi Nagai
- National Research Institute of Fisheries Science, Research Center for Aquatic Genomics, 2-12-4 Fukuura, Kanazawa-ku, Yokohama 236-8648, Kanagawa, Japan.
| | - Shigehiko Miyamoto
- Kaneka Corporation, Medical Device Development Laboratories, 1-8 Mayamae-cho, Takasago 676-8688, Hyogo, Japan
| | - Keita Ino
- Kaneka Corporation, Medical Device Development Laboratories, 1-8 Mayamae-cho, Takasago 676-8688, Hyogo, Japan
| | - Seisuke Tajimi
- Kumamoto Prefectural Fisheries Research Center, 2450-2 Naka, Oyano-machi, Kami-amakusa 869-3603, Kumamoto, Japan
| | - Hiromi Nishi
- Kagoshima Prefectural Fisheries Technology and Development Center, 160-10 Takadaue, Iwamoto, Ibusuki 891-0315, Kagoshima, Japan
| | - Jun Tomono
- Kaneka Corporation, Medical Device Development Laboratories, 1-8 Mayamae-cho, Takasago 676-8688, Hyogo, Japan
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16
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Genovesi B, Berrebi P, Nagai S, Reynaud N, Wang J, Masseret E. Geographic structure evidenced in the toxic dinoflagellate Alexandrium pacificum Litaker (A. catenella - group IV (Whedon & Kofoid) Balech) along Japanese and Chinese coastal waters. MARINE POLLUTION BULLETIN 2015; 98:95-105. [PMID: 26188429 DOI: 10.1016/j.marpolbul.2015.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/29/2015] [Accepted: 07/03/2015] [Indexed: 05/16/2023]
Abstract
The intra-specific diversity and genetic structure within the Alexandrium pacificum Litaker (A. catenella - Group IV) populations along the Temperate Asian coasts, were studied among individuals isolated from Japan to China. The UPGMA dendrogram and FCA revealed the existence of 3 clusters. Assignment analysis suggested the occurrence of gene flows between the Japanese Pacific coast (cluster-1) and the Chinese Zhejiang coast (cluster-2). Human transportations are suspected to explain the lack of genetic difference between several pairs of distant Japanese samples, hardly explained by a natural dispersal mechanism. The genetic isolation of the population established in the Sea of Japan (cluster-3) suggested the existence of a strong ecological and geographical barrier. Along the Pacific coasts, the South-North current allows limited exchanges between Chinese and Japanese populations. The relationships between Temperate Asian and Mediterranean individuals suggested different scenario of large-scale dispersal mechanisms.
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Affiliation(s)
- Benjamin Genovesi
- National Research Institute of Fisheries and Environment of Inland Sea, Research Center for Environmental Conservation, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan; Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD, Université de Montpellier, cc 065, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Patrick Berrebi
- Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD, Université de Montpellier, cc 065, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Satoshi Nagai
- National Research Institute of Fisheries and Environment of Inland Sea, Research Center for Environmental Conservation, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan; National Research Institute of Fisheries Science, Aquatic Genomics Research Center, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Nathalie Reynaud
- National Research Institute of Fisheries and Environment of Inland Sea, Research Center for Environmental Conservation, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan; Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD, Université de Montpellier, cc 065, Place Eugène Bataillon, 34095 Montpellier cedex 05, France
| | - Jinhui Wang
- East China Sea Environmental Monitoring Center, Dong Tang Road 630, Shanghai 200137, PR China
| | - Estelle Masseret
- UMR MARBEC 9190 IRD-Ifremer-UM-CNRS, Université de Montpellier, cc93, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
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17
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Vanormelingen P, Evans KM, Mann DG, Lance S, Debeer AE, D'Hondt S, Verstraete T, De Meester L, Vyverman W. Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites. Mol Ecol 2015; 24:4433-48. [DOI: 10.1111/mec.13336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Pieter Vanormelingen
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
| | - Katharine M. Evans
- School of Geosciences; University of Edinburgh; Edinburgh EH9 3JW UK
- Royal Botanic Garden; Edinburgh EH3 5LR UK
| | - David G. Mann
- Royal Botanic Garden; Edinburgh EH3 5LR UK
- Aquatic Ecosystems; Institute for Food and Agricultural Research and Technology (IRTA); Crta de Poble Nou Km 5.5 E-43540 Sant Carles de la Ràpita Catalunya Spain
| | - Stacey Lance
- Savannah River Ecology Laboratory; University of Georgia; Aiken SC USA
| | - Ann-Eline Debeer
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
| | - Sofie D'Hondt
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
| | - Tine Verstraete
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation; Katholieke Universiteit Leuven; Ch. De Bériotstraat 32 Leuven 3000 Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology; Ghent University; Krijgslaan 281 - S8 Gent 9000 Belgium
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18
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Van den Wyngaert S, Möst M, Freimann R, Ibelings BW, Spaak P. Hidden diversity in the freshwater planktonic diatom Asterionella formosa. Mol Ecol 2015; 24:2955-72. [PMID: 25919789 DOI: 10.1111/mec.13218] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/20/2022]
Abstract
Many freshwater and marine algal species are described as having cosmopolitan distributions. Whether these widely distributed morphologically similar algae also share a similar gene pool remains often unclear. In the context of island biogeography theory, stronger spatial isolation deemed typical of freshwater lakes should restrict gene flow and lead to higher genetic differentiation among lakes. Using nine microsatellite loci, we investigate the genetic diversity of a widely distributed freshwater planktonic diatom, Asterionella formosa, across different lakes in Switzerland and the Netherlands. We applied a hierarchical spatial sampling design to determine the geographical scale at which populations are structured. A subset of the isolates was additionally analysed using amplified fragment length polymorphism (AFLP) markers. Our results revealed complex and unexpected population structure in A. formosa with evidence for both restricted and moderate to high gene flow at the same time. Different genetic markers (microsatellites and AFLPs) analysed with a variety of multivariate methods consistently revealed that genetic differentiation within lakes was much stronger than among lakes, indicating the presence of cryptic species within A. formosa. We conclude that the hidden diversity found in this study is expected to have implications for the further use of A. formosa in biogeographical, conservation and ecological studies. Further research using species-level phylogenetic markers is necessary to place the observed differentiation in an evolutionary context of speciation.
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Affiliation(s)
- S Van den Wyngaert
- Aquatic Ecology, Eawag, Ueberlandstrasse 133, PO Box 611, CH-8600, Duebendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.,Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin, Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - M Möst
- Aquatic Ecology, Eawag, Ueberlandstrasse 133, PO Box 611, CH-8600, Duebendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.,Department of Zoology, University of Cambridge, Downing St., Cambridge, CB2 3EJ, UK
| | - R Freimann
- Institute of Molecular Health Sciences, ETH-Zürich, Otto-Stern-Weg 7, CH-8093, Zürich, Switzerland
| | - B W Ibelings
- Aquatic Ecology, Eawag, Ueberlandstrasse 133, PO Box 611, CH-8600, Duebendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland.,Institut F.-A. Forel, Université de Genève, 10 Route de Suisse, CH-12090, Versoix, Switzerland
| | - P Spaak
- Aquatic Ecology, Eawag, Ueberlandstrasse 133, PO Box 611, CH-8600, Duebendorf, Switzerland.,Institute of Integrative Biology, ETH Zürich, CH-8092, Zürich, Switzerland
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19
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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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20
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Tesson SVM, Montresor M, Procaccini G, Kooistra WHCF. Temporal changes in population structure of a marine planktonic diatom. PLoS One 2014; 9:e114984. [PMID: 25506926 PMCID: PMC4266644 DOI: 10.1371/journal.pone.0114984] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 11/17/2014] [Indexed: 01/17/2023] Open
Abstract
A prevailing question in phytoplankton research addresses changes of genetic diversity in the face of huge population sizes and apparently unlimited dispersal capabilities. We investigated population genetic structure of the pennate planktonic marine diatom Pseudo-nitzschia multistriata at the LTER station MareChiara in the Gulf of Naples (Italy) over four consecutive years and explored possible changes over seasons and from year to year. A total of 525 strains were genotyped using seven microsatellite markers, for a genotypic diversity of 75.05%, comparable to that found in other Pseudo-nitzschia species. Evidence from Bayesian clustering analysis (BA) identified two genetically distinct clusters, here interpreted as populations, and several strains that could not be assigned with ≥90% probability to either population, here interpreted as putative hybrids. Principal Component Analysis (PCA) recovered these two clusters in distinct clouds with most of the putative hybrids located in-between. Relative proportions of the two populations and the putative hybrids remained similar within years, but changed radically between 2008 and 2009 and between 2010 and 2011, when the 2008-population apparently became the dominant one again. Strains from the two populations are inter-fertile, and so is their offspring. Inclusion of genotypes of parental strains and their offspring shows that the majority of the latter could not be assigned to any of the two parental populations. Therefore, field strains classified by BA as the putative hybrids could be biological hybrids. We hypothesize that P. multistriata population dynamics in the Gulf of Naples follows a meta-population-like model, including establishment of populations by cell inocula at the beginning of each growth season and remixing and dispersal governed by moving and mildly turbulent water masses.
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Affiliation(s)
- Sylvie V. M. Tesson
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- * E-mail:
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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21
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Godhe A, Egardt J, Kleinhans D, Sundqvist L, Hordoir R, Jonsson PR. Seascape analysis reveals regional gene flow patterns among populations of a marine planktonic diatom. Proc Biol Sci 2013; 280:20131599. [PMID: 24174105 PMCID: PMC3826216 DOI: 10.1098/rspb.2013.1599] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 10/03/2013] [Indexed: 02/01/2023] Open
Abstract
We investigated the gene flow of the common marine diatom, Skeletonema marinoi, in Scandinavian waters and tested the null hypothesis of panmixia. Sediment samples were collected from the Danish Straits, Kattegat and Skagerrak. Individual strains were established from germinated resting stages. A total of 350 individuals were genotyped by eight microsatellite markers. Conventional F-statistics showed significant differentiation between the samples. We therefore investigated whether the genetic structure could be explained using genetic models based on isolation by distance (IBD) or by oceanographic connectivity. Patterns of oceanographic circulation are seasonally dependent and therefore we estimated how well local oceanographic connectivity explains gene flow month by month. We found no significant relationship between genetic differentiation and geographical distance. Instead, the genetic structure of this dominant marine primary producer is best explained by local oceanographic connectivity promoting gene flow in a primarily south to north direction throughout the year. Oceanographic data were consistent with the significant FST values between several pairs of samples. Because even a small amount of genetic exchange prevents the accumulation of genetic differences in F-statistics, we hypothesize that local retention at each sample site, possibly as resting stages, is an important component in explaining the observed genetic structure.
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Affiliation(s)
- Anna Godhe
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, Gothenburg 405 30, Sweden
| | - Jenny Egardt
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, Gothenburg 405 30, Sweden
| | - David Kleinhans
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, Gothenburg 405 30, Sweden
- Department for Physics, Carl von Ossietzky University Oldenburg, Carl-von-Ossietzky-Strasse 9, Oldenburg 26111, Germany
| | - Lisa Sundqvist
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, Gothenburg 405 30, Sweden
| | - Robinson Hordoir
- Department of Research and Development, Swedish Meteorological and Hydrological Institute, Norrköping 601 76, Sweden
| | - Per R. Jonsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Tjärnö Marine Biological Laboratory, 452 96 Strömstad, Sweden
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22
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Collins S, Rost B, Rynearson TA. Evolutionary potential of marine phytoplankton under ocean acidification. Evol Appl 2013; 7:140-55. [PMID: 24454553 PMCID: PMC3894903 DOI: 10.1111/eva.12120] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 09/12/2013] [Indexed: 01/22/2023] Open
Abstract
Marine phytoplankton have many obvious characters, such as rapid cell division rates and large population sizes, that give them the capacity to evolve in response to global change on timescales of weeks, months or decades. However, few studies directly investigate if this adaptive potential is likely to be realized. Because of this, evidence of to whether and how marine phytoplankton may evolve in response to global change is sparse. Here, we review studies that help predict evolutionary responses to global change in marine phytoplankton. We find limited support from experimental evolution that some taxa of marine phytoplankton may adapt to ocean acidification, and strong indications from studies of variation and structure in natural populations that selection on standing genetic variation is likely. Furthermore, we highlight the large body of literature on plastic responses to ocean acidification available, and evolutionary theory that may be used to link plastic and evolutionary responses. Because of the taxonomic breadth spanned by marine phytoplankton, and the diversity of roles they fill in ocean ecosystems and biogeochemical cycles, we stress the necessity of treating taxa or functional groups individually.
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Affiliation(s)
- Sinéad Collins
- Ashworth Laboratories, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK
| | - Björn Rost
- Alfred Wegener Institute for Polar and Marine Research Bremerhaven, Germany
| | - Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island Narragansett, RI, USA
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Long-range dispersal and high-latitude environments influence the population structure of a "stress-tolerant" dinoflagellate endosymbiont. PLoS One 2013; 8:e79208. [PMID: 24223906 PMCID: PMC3818422 DOI: 10.1371/journal.pone.0079208] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/19/2013] [Indexed: 11/19/2022] Open
Abstract
The migration and dispersal of stress-tolerant symbiotic dinoflagellates (genus Symbiodinium) may influence the response of symbiotic reef-building corals to a warming climate. We analyzed the genetic structure of the stress-tolerant endosymbiont, Symbiodinium glynninomen nudum (ITS2 - D1), obtained from Pocillopora colonies that dominate eastern Pacific coral communities. Eleven microsatellite loci identified genotypically diverse populations with minimal genetic subdivision throughout the Eastern Tropical Pacific, encompassing 1000’s of square kilometers from mainland Mexico to the Galapagos Islands. The lack of population differentiation over these distances corresponds with extensive regional host connectivity and indicates that Pocillopora larvae, which maternally inherit their symbionts, aid in the dispersal of this symbiont. In contrast to its host, however, subtropical populations of S. glynni in the Gulf of California (Sea of Cortez) were strongly differentiated from populations in tropical eastern Pacific. Selection pressures related to large seasonal fluctuations in temperature and irradiance likely explain this abrupt genetic discontinuity. We infer that S. glynni genotypes harbored by host larvae arriving from more southern locations are rapidly replaced by genotypes adapted to more temperate environments. The strong population structure of S. glynni corresponds with fluctuating environmental conditions and suggests that these genetically diverse populations have the potential to evolve rapidly to changing environments and reveals the importance of environmental extremes in driving microbial eukaryote (e.g., plankton) speciation in marine ecosystems.
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24
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A legacy of contrasting spatial genetic structure on either side of the Atlantic-Mediterranean transition zone in a marine protist. Proc Natl Acad Sci U S A 2012; 109:20998-1003. [PMID: 23213247 DOI: 10.1073/pnas.1214398110] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The mechanisms that underpin the varied spatial genetic structures exhibited by free-living marine microorganisms remain controversial, with most studies emphasizing a high dispersal capability that should redistribute genetic diversity in contrast to most macroorganisms whose populations often retain a genetic signature of demographic response to historic climate fluctuations. We quantified the European phylogeographic structure of the marine flagellate Oxyrrhis marina and found a marked difference in spatial genetic structure, population demography, and genetic diversity between the northwest Atlantic and Mediterranean Sea that reflects the persistent separation of these regions as well as context-dependent population responses to contrasting environments. We found similar geographic variation in the level of genetic diversity in the sister species Oxyrrhis maritima. Because the capacity for wide dispersal is not always realized, historic genetic footprints of range expansion and contraction persist in contemporary populations of marine microbes, as they do in larger species. Indeed, the well-described genetic effects of climatic variation on macroorganisms provide clear, testable hypotheses about the processes that drive genetic divergence in marine microbes and thus about the response to future environmental change.
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Richlen ML, Erdner DL, McCauley LAR, Libera K, Anderson DM. Extensive genetic diversity and rapid population differentiation during blooms of Alexandrium fundyense (Dinophyceae) in an isolated salt pond on Cape Cod, MA, USA. Ecol Evol 2012; 2:2588-99. [PMID: 23145343 PMCID: PMC3492784 DOI: 10.1002/ece3.373] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/22/2012] [Accepted: 07/26/2012] [Indexed: 11/24/2022] Open
Abstract
In Massachusetts, paralytic shellfish poisoning (PSP) is annually recurrent along the coastline, including within several small embayments on Cape Cod. One such system, the Nauset Marsh System (NMS), supports extensive marshes and a thriving shellfishing industry. Over the last decade, PSP in the NMS has grown significantly worse; however, the origins and dynamics of the toxic Alexandrium fundyense (Balech) populations that bloom within the NMS are not well known. This study examined a collection of 412 strains isolated from the NMS and the Gulf of Maine (GOM) in 2006-2007 to investigate the genetic characteristics of localized blooms and assess connectivity with coastal populations. Comparisons of genetic differentiation showed that A. fundyense blooms in the NMS exhibited extensive clonal diversity and were genetically distinct from populations in the GOM. In both project years, genetic differentiation was observed among temporal samples collected from the NMS, sometimes occurring on the order of approximately 7 days. The underlying reasons for temporal differentiation are unknown, but may be due, in part, to life-cycle characteristics unique to the populations in shallow embayments, or possibly driven by selection from parasitism and zooplankton grazing; these results highlight the need to investigate the role of selective forces in the genetic dynamics of bloom populations. The small geographic scale and limited connectivity of NMS salt ponds provide a novel system for investigating regulators of blooms, as well as the influence of selective forces on population structure, all of which are otherwise difficult or impossible to study in the adjacent open-coastal waters or within larger estuaries.
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Affiliation(s)
- Mindy L Richlen
- Woods Hole Oceanographic Institution Woods Hole, Massachusetts, 02543
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26
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Nagai S, Itakura S. Specific detection of the toxic dinoflagellates Alexandrium tamarense and Alexandrium catenella from single vegetative cells by a loop-mediated isothermal amplification method. Mar Genomics 2012; 7:43-9. [PMID: 22897962 DOI: 10.1016/j.margen.2012.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 03/06/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
Abstract
In this study, we succeeded in developing a loop-mediated isothermal amplification (LAMP) method that enables sensitive and specific detection of the toxic marine dinoflagellates Alexandrium tamarense and Alexandrium catenella from single cells of both laboratory cultures and naturally blooming cells within 25 min, by monitoring the turbidimeter from the start of the LAMP reaction. The fluorescence intensity was strong enough to allow discrimination between positive and negative results by naked eye under a UV lamp, even in amplified samples from a single cell, by using the LAMP method. Unambiguous detection by naked eye was possible even in half the volume of LAMP cocktail recommended by the manufacturer, suggesting the potential to significantly reduce the cost of Alexandrium monitoring. Therefore, we can conclude that this method is one of the most convenient, sensitive, and cost-effective molecular tools for Alexandrium monitoring.
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Affiliation(s)
- Satoshi Nagai
- National Research Institute of Fisheries and Environment of Inland Sea, Maruishi 2-17-5, Hatsukaichi, Hiroshima 739-0452, Japan.
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Pettay DT, Wham DC, Pinzón JH, LaJeunesse TC. Genotypic diversity and spatial-temporal distribution of Symbiodinium clones in an abundant reef coral. Mol Ecol 2011; 20:5197-212. [PMID: 22082053 PMCID: PMC5957298 DOI: 10.1111/j.1365-294x.2011.05357.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic data are rapidly advancing our understanding of various biological systems including the ecology and evolution of coral-algal symbioses. The fine-scale interactions between individual genotypes of host and symbiont remain largely unstudied and constitute a major gap in knowledge. By applying microsatellite markers developed for both host and symbiont, we investigated the intracolony diversity, prevalence and stability of Symbiodinium glynni (type D1) multilocus genotypes in association with dense populations of Pocillopora at two sites in the Gulf of California. The genetic diversity and allelic frequencies in reef populations of S. glynni remained stable over 3 years. Common clone genotypes persisted over this period, and no temporal population subdivision (Φ(PT) = 0.021 and -0.003) was detected. Collections from circular plots showed no statistical correlation between related Pocillopora individuals and their associations with particular S. glynni genotypes, with no spatial structuring or clonal aggregation across a reef for the symbiont. From permanent linear transects, samples were analysed from multiple locations within a colony and some were resampled approximately 1 year later. Many of these multisampled colonies (approximately 53%) were dominated by a single S. glynni genotype and tended to associate with the same symbiont genotype(s) over time, while colony ramets often possessed unrelated symbiont genotypes. In contrast to the species level, associations between genotypes of Pocillopora and S. glynni are apparently more flexible over space and time. The abundance of sexually recombinant genotypes of S. glynni combined with greater flexibility might provide adaptive mechanisms for these symbioses to evolve rapidly to changes in environmental conditions and allow particular symbiont genotypes to spread through a host population.
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Affiliation(s)
- Daniel T Pettay
- Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA.
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Nagai S. DEVELOPMENT OF A MULTIPLEX PCR ASSAY FOR SIMULTANEOUS DETECTION OF SIX ALEXANDRIUM SPECIES (DINOPHYCEAE) 1. JOURNAL OF PHYCOLOGY 2011; 47:703-708. [PMID: 27022000 DOI: 10.1111/j.1529-8817.2011.00976.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In Japan, the bloom seasons of two toxic species, namely, Alexandrium catenella (Whedon et Kof.) Balech and Alexandrium tamiyavanichii Balech, sometimes overlap with those of three nontoxic Alexandrium species, namely, Alexandrium affine (H. Inouye et Fukuyo) Balech, Alexandrium fraterculus (Balech) Balech, and Alexandrium pseudogoniaulax (Biecheler) T. Horig. ex Y. Kita et Fukuyo. In this study, a multiplex PCR assay has been developed that enables simultaneous detection of six Alexandrium species on the basis of differences in the lengths of the PCR products. The accuracy of the multiplex PCR system was assessed using 101 DNA templates of the six target Alexandrium species and 27 DNA templates of 11 nontarget species (128 DNA templates in total). All amplicons obtained from the 101 DNA templates of the target species were appropriately identified, whereas all 27 DNA templates of the nontarget species were not amplified. Species-specific identification by the multiplex PCR assay was certainly possible from single cells of the target species.
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Affiliation(s)
- Satoshi Nagai
- National Research Institute of Fisheries and Environment of Inland Sea, Maruishi 2-17-5, Hatsukaichi, Hiroshima 739-0452, Japan
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Casabianca S, Penna A, Pecchioli E, Jordi A, Basterretxea G, Vernesi C. Population genetic structure and connectivity of the harmful dinoflagellate Alexandrium minutum in the Mediterranean Sea. Proc Biol Sci 2011; 279:129-38. [PMID: 21593032 DOI: 10.1098/rspb.2011.0708] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The toxin-producing microbial species Alexandrium minutum has a wide distribution in the Mediterranean Sea and causes high biomass blooms with consequences on the environment, human health and coastal-related economic activities. Comprehension of algal genetic differences and associated connectivity is fundamental to understand the geographical scale of adaptation and dispersal pathways of harmful microalgal species. In the present study, we combine A. minutum population genetic analyses based on microsatellites with indirect connectivity (C(i)) estimations derived from a general circulation model of the Mediterranean sea. Our results show that four major clusters of genetically homogeneous groups can be identified, loosely corresponding to four regional seas: Adriatic, Ionian, Tyrrhenian and Catalan. Each of the four clusters included a small fraction of mixed and allochthonous genotypes from other Mediterranean areas, but the assignment to one of the four clusters was sufficiently robust as proved by the high ancestry coefficient values displayed by most of the individuals (>84%). The population structure of A. minutum on this scale can be explained by microalgal dispersion following the main regional circulation patterns over successive generations. We hypothesize that limited connectivity among the A. minutum populations results in low gene flow but not in the erosion of variability within the population, as indicated by the high gene diversity values. This study represents a first and new integrated approach, combining both genetic and numerical methods, to characterize and interpret the population structure of a toxic microalgal species. This approach of characterizing genetic population structure and connectivity at a regional scale holds promise for the control and management of the harmful algal bloom events in the Mediterranean Sea.
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Affiliation(s)
- Silvia Casabianca
- Department of Biomolecular Sciences, University of Urbino, Pesaro 61121, Italy
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Hundred years of genetic structure in a sediment revived diatom population. Proc Natl Acad Sci U S A 2011; 108:4252-7. [PMID: 21282612 DOI: 10.1073/pnas.1013528108] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
This paper presents research on the genetic structure and diversity of populations of a common marine protist and their changes over time. The bloom-forming diatom Skeletonema marinoi was used as a model organism. Strains were revived from anoxic discrete layers of a (210)Pb-dated sediment core accumulated over more than 100 y, corresponding to >40,000 diatom mitotic generations. The sediment core was sampled from the highly eutrophic Mariager Fjord in Denmark. The genetic structure of S. marinoi was examined using microsatellite markers, enabling exploration of changes through time and of the effect of environmental fluctuations. The results showed a stable population structure among and within the examined sediment layers, and a similar genetic structure has been maintained over thousands of generations. However, established populations from inside the fjord were highly differentiated from open-sea populations. Despite constant water exchange and influx of potential colonizers into the fjord, the populations do not mix. One fjord population, accumulated in 1980, was significantly differentiated from the other groups of strains isolated from the fjord. This differentiation could have resulted from the status of Mariager Fjord, which was considered hypereutrophic, around 1980. There was no significant genetic difference between pre- and posteutrophication groups of strains. Our data show that dispersal potential and generation time do not have a large impact on the genetic structuring of the populations investigated here. Instead, the environmental conditions, such as the extreme eutrophication of the Mariager Fjord, are deemed more important.
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Lowe CD, Montagnes DJS, Martin LE, Watts PC. High genetic diversity and fine-scale spatial structure in the marine flagellate Oxyrrhis marina (Dinophyceae) uncovered by microsatellite loci. PLoS One 2010; 5:e15557. [PMID: 21203414 PMCID: PMC3009739 DOI: 10.1371/journal.pone.0015557] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 11/12/2010] [Indexed: 11/18/2022] Open
Abstract
Free-living marine protists are often assumed to be broadly distributed and genetically homogeneous on large spatial scales. However, an increasing application of highly polymorphic genetic markers (e.g., microsatellites) has provided evidence for high genetic diversity and population structuring on small spatial scales in many free-living protists. Here we characterise a panel of new microsatellite markers for the common marine flagellate Oxyrrhis marina. Nine microsatellite loci were used to assess genotypic diversity at two spatial scales by genotyping 200 isolates of O. marina from 6 broad geographic regions around Great Britain and Ireland; in one region, a single 2 km shore line was sampled intensively to assess fine-scale genetic diversity. Microsatellite loci resolved between 1-6 and 7-23 distinct alleles per region in the least and most variable loci respectively, with corresponding variation in expected heterozygosities (H(e)) of 0.00-0.30 and 0.81-0.93. Across the dataset, genotypic diversity was high with 183 genotypes detected from 200 isolates. Bayesian analysis of population structure supported two model populations. One population was distributed across all sampled regions; the other was confined to the intensively sampled shore, and thus two distinct populations co-occurred at this site. Whilst model-based analysis inferred a single UK-wide population, pairwise regional F(ST) values indicated weak to moderate population sub-division (0.01-0.12), but no clear correlation between spatial and genetic distance was evident. Data presented in this study highlight extensive genetic diversity for O. marina; however, it remains a substantial challenge to uncover the mechanisms that drive genetic diversity in free-living microorganisms.
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Affiliation(s)
- Chris D Lowe
- School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom.
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GODHE ANNA, HÄRNSTRÖM KAROLINA. Linking the planktonic and benthic habitat: genetic structure of the marine diatom Skeletonema marinoi. Mol Ecol 2010; 19:4478-90. [DOI: 10.1111/j.1365-294x.2010.04841.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
The role of geographic isolation in marine microbial speciation is hotly debated because of the high dispersal potential and large population sizes of planktonic microorganisms and the apparent lack of strong dispersal barriers in the open sea. Here, we show that gene flow between distant populations of the globally distributed, bloom-forming diatom species Pseudo-nitzschia pungens (clade I) is limited and follows a strong isolation by distance pattern. Furthermore, phylogenetic analysis implies that under appropriate geographic and environmental circumstances, like the pronounced climatic changes in the Pleistocene, population structuring may lead to speciation and hence may play an important role in diversification of marine planktonic microorganisms. A better understanding of the factors that control population structuring is thus essential to reveal the role of allopatric speciation in marine microorganisms.
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