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Wang C, Gu J, Li W, Wang J, Wang Z, Lin Q. Metabarcoding reveals a high diversity and complex eukaryotic microalgal community in coastal waters of the northern Beibu Gulf, China. Front Microbiol 2024; 15:1403964. [PMID: 38903786 PMCID: PMC11188352 DOI: 10.3389/fmicb.2024.1403964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
Beibu Gulf is an important semi-enclosed bay located in the northwestern South China Sea, and is famous for its high bio-productivity and rich bio-diversity. The fast development along the Beibu Gulf Economical Rim has brought pressure to the environment, and algal blooms occurred frequently in the gulf. In this study, surface water samples and micro-plankton samples (20-200 μm) were collected in the northern Beibu Gulf coast. Diversity and distribution of eukaryotic planktonic microalgae were analyzed by both metabarcoding and microscopic analyses. Metabarcoding revealed much higher diversity and species richness of microalgae than morphological observation, especially for dinoflagellates. Metabarcoding detected 144 microalgal genera in 8 phyla, while microscopy only detected 40 genera in 2 phyla. The two methods revealed different microalgal community structures. Dinoflagellates dominated in microalgal community based on metabarcoding due to their high copies of 18 s rRNA gene, and diatoms dominated under microscopy. Altogether 48 algal bloom and/or toxic species were detected in this study, 34 species by metabarcoding and 19 species by microscopy. Our result suggested a high potential risk of HABs in the Beibu Gulf. Microalgal community in the surface water samples demonstrated significantly higher OTU/species richness, alpha diversity, and abundance than those in the micro-plankton samples, although more HAB taxa were detected by microscopic observations in the micro-plankton samples. Furthermore, nano-sized taxa, such as those in chlorophytes, haptophytes, and chrysophyceans, occurred more abundantly in the surface water samples. This study provided a comprehensive morphological and molecular description of microalgal community in the northern Beibu Gulf.
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Affiliation(s)
| | | | | | | | - Zhaohui Wang
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qiuqi Lin
- College of Life Science and Technology, Jinan University, Guangzhou, China
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Wang H, Liu K, He Z, Chen Y, Hu Z, Chen W, Leaw CP, Chen N. Extensive intragenomic variations of the 18S rDNA V4 region in the toxigenic diatom species Pseudo-nitzschia multistriata revealed through high-throughput sequencing. MARINE POLLUTION BULLETIN 2024; 201:116198. [PMID: 38428045 DOI: 10.1016/j.marpolbul.2024.116198] [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: 11/11/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
Metabarcoding analysis is an effective technique for monitoring the domoic acid-producing Pseudo-nitzschia species in marine environments, uncovering high-levels of molecular diversity. However, such efforts may result in the overinterpretation of Pseudo-nitzschia species diversity, as molecular diversity not only encompasses interspecies and intraspecies diversities but also exhibits extensive intragenomic variations (IGVs). In this study, we analyzed the V4 region of the 18S rDNA of 30 strains of Pseudo-nitzschia multistriata collected from the coasts of China. The results showed that each P. multistriata strain harbored about a hundred of unique 18S rDNA V4 sequence varieties, of which each represented by a unique amplicon sequence variant (ASV). This study demonstrated the extensive degree of IGVs in P. multistriata strains, suggesting that IGVs may also present in other Pseudo-nitzschia species and other phytoplankton species. Understanding the scope and levels of IGVs is crucial for accurately interpreting the results of metabarcoding analysis.
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Affiliation(s)
- Hui Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ziyan He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- Department of Aquaculture, College of Fisheries, Guangdong Ocean University, Zhanjiang, Guangdong 524088, China
| | - Weizhou Chen
- Institution of Marine Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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Rishan ST, Kline RJ, Rahman MS. Exploitation of environmental DNA (eDNA) for ecotoxicological research: A critical review on eDNA metabarcoding in assessing marine pollution. CHEMOSPHERE 2024; 351:141238. [PMID: 38242519 DOI: 10.1016/j.chemosphere.2024.141238] [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: 07/04/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
The rise in worldwide population has led to a noticeable spike in the production, consumption, and transportation of energy and food, contributing to elevated environmental pollution. Marine pollution is a significant global environmental issue with ongoing challenges, including plastic waste, oil spills, chemical pollutants, and nutrient runoff, threatening marine ecosystems, biodiversity, and human health. Pollution detection and assessment are crucial to understanding the state of marine ecosystems. Conventional approaches to pollution evaluation usually represent laborious and prolonged physical and chemical assessments, constraining their efficacy and expansion. The latest advances in environmental DNA (eDNA) are valuable methods for the detection and surveillance of pollution in the environment, offering enhanced sensibility, efficacy, and involvement. Molecular approaches allow genetic information extraction from natural resources like water, soil, or air. The application of eDNA enables an expanded evaluation of the environmental condition by detecting both identified and unidentified organisms and contaminants. eDNA methods are valuable for assessing community compositions, providing indirect insights into the intensity and quality of marine pollution through their effects on ecological communities. While eDNA itself is not direct evidence of pollution, its analysis offers a sensitive tool for monitoring changes in biodiversity, serving as an indicator of environmental health and allowing for the indirect estimation of the impact and extent of marine pollution on ecosystems. This review explores the potential of eDNA metabarcoding techniques for detecting and identifying marine pollutants. This review also provides evidence for the efficacy of eDNA assessment in identifying a diverse array of marine pollution caused by oil spills, harmful algal blooms, heavy metals, ballast water, and microplastics. In this report, scientists can expand their knowledge and incorporate eDNA methodologies into ecotoxicological research.
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Affiliation(s)
- Sakib Tahmid Rishan
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Richard J Kline
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA
| | - Md Saydur Rahman
- Biochemistry and Molecular Biology Program, School of Integrative Biological and Chemical Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA; School of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Brownsville, Texas, USA.
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Liu K, Huang X, Ding X, Chen N. The high molecular diversity in Noctiluca scintillans is dominated by intra-genomic variations revealed by single cell high-throughput sequencing of 18S rDNA V4. HARMFUL ALGAE 2024; 132:102568. [PMID: 38331542 DOI: 10.1016/j.hal.2024.102568] [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: 10/30/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024]
Abstract
The application of high-throughput sequencing (HTS) technologies has revolutionized research on phytoplankton biodiversity by generating an unprecedented amount of molecular data in marine ecosystem surveys. However, high-level of molecular diversity uncovered in HTS-based metabarcoding analyses may lead to overinterpretation of phytoplankton diversity due to excessive intra-genomic variations (IGVs). The aims in this study are to explore the nature of phytoplankton molecular diversity and to test the hypothesis. We carried out single-cell metabarcoding analysis of 18S rDNA V4 sequences obtained in single Noctiluca scintillans cells isolated from various sites in coastal waters of China. Results showed that each single N. scintillans cell harbored a high level of IGVs with about 100 amplicon sequence variants (ASVs). The large numbers of non-dominant ASVs identified in N. scintillans cells, which might correspond to the larger numbers of ASVs annotated as N. scintillans and showed similar temporal dynamics in metabarcoding analyses, could inflate the inter-species diversity or intra-species genetic diversity. In addition, there were large numbers of additional ASVs that were not annotated as N. scintillans. These non-N. scintillans ASVs might represent diverse preys for N. scintillans, consistent with previous reports that N. scintillans may act as chance predator of a broad-spectrum preys. This single-cell study has unambiguously demonstrated that the existence of high levels of IGVs in N. scintillans and most likely many other phytoplankton species, demonstrating that the majority of the molecular diversity revealed in metabarcoding analysis, which were generally interpreted as the sum of inter-species diversity and intra-species diversity, actually included high levels of IGVs and should be interpreted with caution.
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Affiliation(s)
- Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xianliang Huang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiangxiang Ding
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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Liu K, Liu S, Cui Z, Zhao Y, Chen N. Rich diversity and active spatial-temporal dynamics of Thalassiosira species revealed by time-series metabarcoding analysis. ISME COMMUNICATIONS 2024; 4:ycad009. [PMID: 38313810 PMCID: PMC10837834 DOI: 10.1093/ismeco/ycad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 02/06/2024]
Abstract
Thalassiosira is a species-rich genus in Bacillariophyta that not only contributes positively as primary producer, but also poses negative impacts on ecosystems by causing harmful algal blooms. Although taxonomical studies have identified a large number of Thalassiosira species, however, the composition of Thalassiosira species and their geographical distribution in marine ecosystems were not well understood due primarily to the lack of resolution of morphology-based approaches used previously in ecological expeditions. In this study, we systematically analyzed the composition and spatial-temporal dynamic distributions of Thalassiosira in the model marine ecosystem Jiaozhou Bay by applying metabarcoding analysis. Through analyzing samples collected monthly from 12 sampling sites, 14 Thalassiosira species were identified, including five species that were not previously reported in Jiaozhou Bay, demonstrating the resolution and effectiveness of metabarcoding analysis in ecological research. Many Thalassiosira species showed prominent temporal preferences in Jiaozhou Bay, with some displaying spring-winter preference represented by Thalassiosira tenera, while others displaying summer-autumn preference represented by Thalassiosira lundiana and Thalassiosira minuscula, indicating that the temperature is an important driving factor in the temporal dynamics. The application of metabarcoding analysis, equipped with appropriate molecular markers with high resolution and high specificity and databases of reference molecular marker sequences for potential all Thalassiosira species, will revolutionize ecological research of Thalassiosira species in Jiaozhou Bay and other marine ecosystems.
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Affiliation(s)
- Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zongmei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yongfang Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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Huang Z, Pan B, Zhao X, Liu X, Liu X, Zhao G. Hydrological disturbances enhance stochastic assembly processes and decrease network stability of algae communities in a highland floodplain system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166207. [PMID: 37567295 DOI: 10.1016/j.scitotenv.2023.166207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/19/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Floodplains are hotspots for biodiversity research and conservation worldwide. Hydrological disturbances can profoundly influence the ecological processes and functions of floodplain systems by altering key biological groups such as algae communities. However, the impacts of flood disturbance on the assembly processes and co-occurrence patterns of algae communities in floodplain ecosystems are still unclear. To ascertain the response patterns of algae communities to flood disturbance, we characterized planktonic and benthic algae communities in 144 water and sediment samples collected from the Tibetan floodplain during non-flood and flood periods based on 23S ribosomal RNA gene sequencing. Results showed that planktonic algae exhibited higher diversity and greater compositional variations compared with benthic communities after flood disturbance. Flooding promoted algae community homogenization at horizontal (rivers vs. oxbow lakes) and vertical levels (water vs. sediment). Stochastic processes governed the assembly of distinct algae communities, and their ecological impacts were enhanced in response to flooding. In the non-flood period, dispersal limitation (81.78 %) was the primary ecological process driving algae community assembly. In the flood period, the relative contribution of ecological drift (72.91 %) to algae community assembly markedly increased, with dispersal limitation (22.61 %) being less important. Flooding reduced the interactions among algae taxa, resulting in lower network complexity and stability. Compared with the planktonic algae subnetworks, the benthic subnetworks showed greater stability in the face of flooding. Findings of this study broaden our understanding of how algae communities respond to hydrological disturbances from an ecological perspective and could be useful for the management of highland floodplain ecosystems.
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Affiliation(s)
- Zhenyu Huang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Baozhu Pan
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Xiaohui Zhao
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Xing Liu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Xinyuan Liu
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
| | - Gengnan Zhao
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, Xi'an, Shaanxi 710048, PR China.
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Yu Z, Tang Y, Gobler CJ. Harmful algal blooms in China: History, recent expansion, current status, and future prospects. HARMFUL ALGAE 2023; 129:102499. [PMID: 37951615 DOI: 10.1016/j.hal.2023.102499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/28/2023] [Accepted: 09/02/2023] [Indexed: 11/14/2023]
Abstract
The impacts of harmful algal blooms (HABs) on economies, public health, ecosystems, and aquaculture across the globe have all increased in recent decades, and this has been acutely the case in China. Here, we review the history of HABs and HABs research in China, as well as recent trends in HABs and future prospects of HAB science in China. The most updated analyses demonstrated that the number of HAB events, the number of HAB species, the aerial coverage of HABs, and the impacts of HABs in Chinese waters during the 21st century were all higher than that during the last two decades of the 20th century. The increase in the number of HABs in China has been significantly correlated with the increased discharge of ammonium and total phosphorus into coastal waters (p < 0.01 for both). Notable newly recognized events this century have included chronic HABs caused by Prorocentrum donghaiense and Karenia mikimotoi, a paralytic shellfish poisoning event caused by Gymnodinium catenatum that sickened 80 people, brown tides caused by Aureococcus anophagefferens, green tides caused by Ulva prolifera, golden tides caused by Sargassum horneri, and the disruption of a nuclear power plant caused by a bloom of Phaeocystis globosa. A series of key discoveries regarding HABs has been made this century including documentation of nearly all known HAB toxins in Chinese waters, discovery of novel cyst-formation and/or life stages of multiple HABs-causing species, identification of the chemical and physical oceanographic drivers of multiple HABs including those formed by P. donghaiense, K. mikimotoi, and U. prolifera, and the successful mitigation of HABs via the use of modified clay approaches. Future research prospects highlighted include the use of macroalgae as a means to prevent, mitigate, and control (PCM) HABs and the process by which multi-disciplinary studies involving molecular approaches (omics), remote in situ detection, artificial intelligence, and mega-data analyses might be used to develop refined and realistic HAB forecasting platforms. Collectively, this review demonstrates the significant evolution of HAB science since the 20th century in China and demonstrates that while HABs in China are complex and widespread, recent and on-going discoveries make the development of detailed understanding and effective measures to mitigate the negative effects of HABs a hopeful outcome in the coming years.
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Affiliation(s)
- Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Yingzhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790, United States of America
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Zhu Y, Wang Z, Song L, Gu J, Ye Z, Jin R, Wu J. Spatiotemporal variation of phytoplankton communities and water quality among seaweed, shellfish and cage fish culture systems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165305. [PMID: 37406709 DOI: 10.1016/j.scitotenv.2023.165305] [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: 01/16/2023] [Revised: 06/19/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
Various marine aquaculture systems have different impacts on the environment, but few assessments were focused on the environmental impact by different systems in the same region. To study the effects of various aquaculture systems on phytoplankton community structure and water properties, 5 surveys were carried out in seaweed (Gracilaria lemaneiformis, GL), shellfish (Mytilus coruscus, MC) and cage fish (Larimichthys crocea, LC) mariculture areas in Dongji island, Zhejiang, China from June to September 2020. Significant differences were observed in some environmental parameters and phytoplankton communities among three aquaculture systems. The dissolved oxygen concentrations and Secchi depth in the surface waters in GL area were relatively higher than in the blank and other areas. As for nutrients concentration, LC and MC areas had higher concentrations than blank area, while GL area was the lowest. Though Chlorophyll-a concentration displayed fluctuations, relatively lower concentrations were found in GL area. Shannon diversity index was found to be relatively constant and higher in GL area. The Non-metric multidimensional scaling results revealed that phytoplankton composition had a distinct pattern among sampling times. The correlations and Redundancy analysis showed that total nitrogen, salinity and transparency were primary environmental factors associated with phytoplankton composition. Our study confirmed that different marine aquaculture systems can cause environmental fluctuations. Among the three systems, seaweed cultivation can bring multiple positive effects by improving surrounding water quality and increasing the phytoplankton composition. G. lemaneiformis culture in summer has great positive impact on seawater environment as it can maintain the ecological balance and reduce the risk of harmful algal blooms (HABs), and therefore, it is strongly recommended more G. lemaneiformis cultivation in this region in summer.
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Affiliation(s)
- Yaojia Zhu
- Zhejiang University, Ocean College, Zhoushan, Zhejiang 316021, China
| | - Zhiyin Wang
- Zhejiang University, Ocean College, Zhoushan, Zhejiang 316021, China
| | - Li Song
- Zhejiang University, Ocean College, Zhoushan, Zhejiang 316021, China
| | - Jiali Gu
- Zhejiang University, Ocean College, Zhoushan, Zhejiang 316021, China
| | - Zhanjiang Ye
- Zhejiang University, Ocean College, Zhoushan, Zhejiang 316021, China
| | - Runjie Jin
- Zhejiang University, Ocean College, Zhoushan, Zhejiang 316021, China
| | - Jiaping Wu
- Zhejiang University, Ocean College, Zhoushan, Zhejiang 316021, China.
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Bilbao J, Pavloudi C, Blanco-Rayón E, Franco J, Madariaga I, Seoane S. Phytoplankton community composition in relation to environmental variability in the Urdaibai estuary (SE Bay of Biscay): Microscopy and eDNA metabarcoding. MARINE ENVIRONMENTAL RESEARCH 2023; 191:106175. [PMID: 37717336 DOI: 10.1016/j.marenvres.2023.106175] [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: 06/21/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023]
Abstract
Phytoplankton monitoring is essential for the global understanding of aquatic ecosystems. The present research studies the phytoplankton community of the Urdaibai estuary, combining microscopy and eDNA metabarcoding for the first time in the area. The main aims were to describe the phytoplankton community composition in relation to the environmental conditions of the estuary, and to compare the two methods used. Diatoms Minutocellus polymorphus and Chaetoceros tenuissimus dominated the outer estuary, being replaced by Teleaulax acuta (cryptophyte), Kryptoperidinium foliaceum (dinoflagellate) and Cyclotella spp. (diatom) towards the inner area. This change was mainly prompted by salinity and nutrients. Metabarcoding revealed the presence of 223 species that were not observed by microscopy in previous studies in the estuary. However, several characteristic species (e.g., K. foliaceum) were only detected with microscopy. Additionally, microscopy covered the limitations of eDNA metabarcoding concerning quantification. Thus, to give a full insight, a combination of techniques is recommended.
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Affiliation(s)
- Jone Bilbao
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain.
| | - Christina Pavloudi
- Institute of Marine Biology, Biotechnology, Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion, Crete, Greece; Department of Biological Sciences, The George Washington University, District of Columbia, USA
| | - Esther Blanco-Rayón
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain
| | | | - Iosu Madariaga
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Sergio Seoane
- Department of Plant Biology and Ecology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain; Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE- UPV/EHU), University of the Basque Country, UPV/EHU, Plentzia, Spain
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10
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Xiaodong L, Weijing L, Fan J, Ziqin C, Yang C, Ziyang W, Tan Y, Jing L, Weicheng W, Xinhua C. The dinoflagellate Noctiluca scintillans in China: A review of its distribution and role in harmful algal blooms. MARINE POLLUTION BULLETIN 2023; 194:115415. [PMID: 37634317 DOI: 10.1016/j.marpolbul.2023.115415] [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: 07/04/2023] [Revised: 08/07/2023] [Accepted: 08/12/2023] [Indexed: 08/29/2023]
Abstract
The dinoflagellate Noctiluca scintillans is often reported as a worldwide HAB species and caused severe financial losses to local aquaculture. In this review, we summarized the temporal and geographical distribution of its HABs in China, as well as its position in the plankton structure. Increasing N. scintillans HABs, both frequency and coverage, have broken out in almost all Chinese coastal regions mainly from April to June, with short-term and small coverage blooms as the primary type. The HAB period seems to shift with age and latitude. Recently, increasing abundance and dominance of N. scintillans were also reported in plankton communities in Chinese coastal waters, with multiple environmental factors related. In particular, trophic relationships may play an important role in its dominance and outbreaks of HABs. However, how N. scintillans became a dominant species in China and the mechanisms responsible for its HABs require further study.
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Affiliation(s)
- Li Xiaodong
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China.
| | - Lu Weijing
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China
| | - Jiang Fan
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China
| | - Chen Ziqin
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China
| | - Chang Yang
- College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China
| | - Wang Ziyang
- College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China
| | - Yan Tan
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong Province 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266071, China; Centre for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Li Jing
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Wang Weicheng
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China
| | - Chen Xinhua
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, College of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China; Fuzhou Institute of Oceanography, Fuzhou 350108, China
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11
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Bernard E, Guéguen C. Molecular changes in phenolic compounds in Euglena gracilis cells grown under metal stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1099375. [PMID: 37229138 PMCID: PMC10203486 DOI: 10.3389/fpls.2023.1099375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
Metal presence in the aquatic ecosystem has increased and diversified over the last decades due to anthropogenic sources. These contaminants cause abiotic stress on living organisms that lead to the production of oxidizing molecules. Phenolic compounds are part of the defense mechanisms countering metal toxicity. In this study, the production of phenolic compounds by Euglena gracilis under three different metal stressors (i.e. cadmium, copper, or cobalt) at sub-lethal concentration was assessed using an untargeted metabolomic approach by mass spectrometry combined with neuronal network analysis (i.e. Cytoscape). The metal stress had a greater impact on molecular diversity than on the number of phenolic compounds. The prevalence of sulfur- and nitrogen-rich phenolic compounds were found in Cd- and Cu-amended cultures. Together these results confirm the impact of metallic stress on phenolic compounds production, which could be utilized to assess the metal contamination in natural waters.
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12
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He L, Yu Z, Xu X, Zhu J, Yuan Y, Cao X, Song X. Metabarcoding analysis identifies high diversity of harmful algal bloom species in the coastal waters of the Beibu Gulf. Ecol Evol 2023; 13:e10127. [PMID: 37223313 PMCID: PMC10202623 DOI: 10.1002/ece3.10127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 05/25/2023] Open
Abstract
Harmful algal blooms (HABs) have occurred more frequently in recent years. In this study, to investigate their potential impact in the Beibu Gulf, short-read and long-read metabarcoding analyses were combined for annual marine phytoplankton community and HAB species identification. Short-read metabarcoding showed a high level of phytoplankton biodiversity in this area, with Dinophyceae dominating, especially Gymnodiniales. Multiple small phytoplankton, including Prymnesiophyceae and Prasinophyceae, were also identified, which complements the previous lack of identifying small phytoplankton and those unstable after fixation. Of the top 20 phytoplankton genera identified, 15 were HAB-forming genera, which accounted for 47.3%-71.5% of the relative abundance of phytoplankton. Based on long-read metabarcoding, a total of 147 OTUs (PID > 97%) belonging to phytoplankton were identified at the species level, including 118 species. Among them, 37 species belonged to HAB-forming species, and 98 species were reported for the first time in the Beibu Gulf. Contrasting the two metabarcoding approaches at the class level, they both showed a predominance of Dinophyceae, and both included high abundances of Bacillariophyceae, Prasinophyceae, and Prymnesiophyceae, but the relative contents of the classes varied. Notably, the results of the two metabarcoding approaches were quite different below the genus level. The high abundance and diversity of HAB species were probably due to their special life history and multiple nutritional modes. Annual HAB species variation revealed in this study provided a basis for evaluating their potential impact on aquaculture and even nuclear power plant safety in the Beibu Gulf.
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Affiliation(s)
- Liyan He
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Functional Laboratory of Marine Ecology and Environmental ScienceLaoshan LaboratoryQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Functional Laboratory of Marine Ecology and Environmental ScienceLaoshan LaboratoryQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin Xu
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Functional Laboratory of Marine Ecology and Environmental ScienceLaoshan LaboratoryQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Jianan Zhu
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Functional Laboratory of Marine Ecology and Environmental ScienceLaoshan LaboratoryQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Yongquan Yuan
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Functional Laboratory of Marine Ecology and Environmental ScienceLaoshan LaboratoryQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Xihua Cao
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Functional Laboratory of Marine Ecology and Environmental ScienceLaoshan LaboratoryQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
| | - Xiuxian Song
- CAS Key Laboratory of Marine Ecology and Environmental SciencesInstitute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Functional Laboratory of Marine Ecology and Environmental ScienceLaoshan LaboratoryQingdaoChina
- Center for Ocean Mega‐ScienceChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
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13
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Zhang K, Zheng S, Liang J, Zhao Y, Li Q, Zhu M, Dai S, Sun X. Microplastic load of benthic fauna in Jiaozhou Bay, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 320:121073. [PMID: 36641062 DOI: 10.1016/j.envpol.2023.121073] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 06/17/2023]
Abstract
The prevalence of microplastic pollution in the ocean has caused widespread concern. Many studies have focused on the occurrence of microplastics in the marine environment and organisms, but the fate of microplastics in the ocean is still unclear, and the factors affecting the distribution of microplastics have not yet been consistently concluded. The aims of this study were to estimate the load of microplastics in benthic organisms as a temporary storage and to analyze the factors affecting microplastic ingestion by benthic organisms. For the purpose of this study, the benthic organisms in Jiaozhou Bay, China, were collected quarterly and were divided into the following six groups: polychaetes, mollusks, crustaceans, echinoderms, fish, and others. We concluded that the microplastic abundance in the benthos in Jiaozhou Bay was 1.00 ± 0.11 items/ind. (15.5 ± 3.5 items/g). The total load of microplastics in the benthic fauna in the bay with an area of 374 km2 was estimated to be 36.4 kg. On an individual basis, the fish contained significantly more microplastics than the other taxa. Furthermore, the characteristics of the microplastics in the benthic organisms were mainly fibrous, black, polyethylene, and <500 μm in size. In addition, the microplastic ingestion by benthic organisms was regulated by multiple factors, including biological characteristics and the environment. The masses of the organisms, the ambient seawater and sediment, and the spatial variations all influenced the microplastic ingestion by the organisms. The results of this study demonstrate that benthic organisms are an important storage for microplastics as they transferred through the ocean, and they provide an unbiased comparison of microplastic pollution among multiple organisms and the relevant pollution factors.
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Affiliation(s)
- Kangning Zhang
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shan Zheng
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Junhua Liang
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yongfang Zhao
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qingjie Li
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Mingliang Zhu
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Sheng Dai
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxia Sun
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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14
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Liu X, Liu Y, Chai Z, Hu Z, Tang YZ. A combined approach detected novel species diversity and distribution of dinoflagellate cysts in the Yellow Sea, China. MARINE POLLUTION BULLETIN 2023; 187:114567. [PMID: 36640495 DOI: 10.1016/j.marpolbul.2022.114567] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Resting cysts of dinoflagellates seed harmful algal blooms (HABs) and their geographic expansion, which makes it fundamentally important to obtain comprehensive inventories of dinoflagellate resting cysts in HABs-prone regions. The Yellow Sea (YS) of China has observed numerous outbreaks of dinoflagellate HABs with some novel species recorded recently indicating an underestimated HABs-causing species diversity. We report our investigation of dinoflagellate cysts of YS via an approach combining metabarcoding sequencing and single-cyst morpho-molecular identification, which identified many novel cyst species and a significant controlling effect of the Yellow Sea Cold Water Mass on cyst composition. The metabarcoding and single cyst-based sequencing detected 11 cyst species never being unambiguously reported in China, 10 never reported as cyst producers, and 3 HABs-causing species never reported from YS. Our detections of many potentially toxic or HABs-causative, particularly novel, cysts and distribution pattern provide important insights into the risks and ecology of dinoflagellate HABs.
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Affiliation(s)
- Xiaohan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhaoyang Chai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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15
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Gaonkar CC, Campbell L. Metabarcoding reveals high genetic diversity of harmful algae in the coastal waters of Texas, Gulf of Mexico. HARMFUL ALGAE 2023; 121:102368. [PMID: 36639185 DOI: 10.1016/j.hal.2022.102368] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/10/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Environmental-DNA (eDNA) for metabarcoding is a rapid and effective means to investigate microplankton community composition and species diversity. The objective of this study was to examine the genetic diversity of the phytoplankton community in the Gulf of Mexico, with particular emphasis on harmful algal bloom species. Samples were collected at stations along the coast of Texas in September-October 2017 that were inundated by low salinity waters in the aftermath of Hurricane Harvey. Metabarcodes were generated from the eDNA targeting both the V4 and V8-V9 regions of the 18S rDNA gene. Evaluation of the metabarcodes revealed an unexpectedly high number of harmful algal species during this short period, including five that had not been documented in this region previously. A total of 36 harmful algal species could be differentiated based on V4 and V8-V9 metabarcode markers. Using a phylogenetic approach, the taxonomic resolution of each marker differed and not all species could be differentiated using solely one marker. The V4 region resolved species within some genera (e.g., Heterocapsa), while the V8-V9 marker was necessary to resolve species within other genera (e.g., Chattonella). In other cases, species differentiation within a genus required a combination of both markers (e.g., Prorocentrum, Karenia), or another marker will be needed to resolve all species (e.g., Alexandrium, Dinophysis). We conclude that no single marker can delineate all species, so it is recommended HAB monitoring programs use more than one marker. Overall, the observed diversity of HAB species along the Texas coast using metabarcoding exceeded reports from other parts of the world.
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Affiliation(s)
- Chetan C Gaonkar
- Department of Oceanography, Texas A&M University, College Station, TX 77843, USA
| | - Lisa Campbell
- Department of Oceanography, Texas A&M University, College Station, TX 77843, USA.
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16
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Boudriga I, Abdennadher M, Khammeri Y, Mahfoudi M, Quéméneur M, Hamza A, Bel Haj Hmida N, Zouari AB, Hassen MB. Karenia selliformis bloom dynamics and growth rate estimation in the Sfax harbour (Tunisia), by using automated flow cytometry equipped with image in flow, during autumn 2019. HARMFUL ALGAE 2023; 121:102366. [PMID: 36639188 DOI: 10.1016/j.hal.2022.102366] [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: 04/19/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
A Karenia selliformis bloom event in the Gulf of Gabès (Mediterranean Sea), was monitored over 9 days at high frequency during fall 2019, by using an automated flow cytometer (Cytosense, Cytobuoy b.v.) with an image-in-flow attachment. The instrument recorded the shape of the optical signals that lead to the resolution of six cell groups of pico-, nano- and microphytoplankton, during the Harmful Algal Bloom (HAB). K. selliformis cell dimensions derived from the hourly records, enabled to estimate the daily division rate over the bloom period. Results revealed that K. selliformis was the only bloom-forming species and it reached its highest mean abundance the fourth day of the survey. A shift in the nutrient composition occurred with a potential P limitation during the bloom growth and N limitation during the bloom collapse. The co-inertia analysis revealed opposite patterns for K. selliformis and heterotrophic prokaryotes suggesting trophic interactions and possible mixotrophic behaviour of K. selliformis at the end of the bloom. K. selliformis exhibited low growth rates generally < 1 division day-1, which could not explain the observed high abundance. The tide played a crucial role in the dynamics of K. selliformis at a semi-diurnal scale and at spring-neap tide scale and was probably enhancing K. selliformis accumulation.
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Affiliation(s)
- Ismail Boudriga
- INSTM - Institut National des Sciences et Technologies de la Mer, Tunisia.
| | | | - Yosra Khammeri
- INSTM - Institut National des Sciences et Technologies de la Mer, Tunisia
| | - Mabrouka Mahfoudi
- INSTM - Institut National des Sciences et Technologies de la Mer, Tunisia
| | - Marianne Quéméneur
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Asma Hamza
- INSTM - Institut National des Sciences et Technologies de la Mer, Tunisia
| | | | | | - Malika Bel Hassen
- INSTM - Institut National des Sciences et Technologies de la Mer, Tunisia
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17
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Wang Z, Liu L, Tang Y, Li A, Liu C, Xie C, Xiao L, Lu S. Phytoplankton community and HAB species in the South China Sea detected by morphological and metabarcoding approaches. HARMFUL ALGAE 2022; 118:102297. [PMID: 36195422 DOI: 10.1016/j.hal.2022.102297] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 07/23/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
The southern Chinese coast is one of the most developed regions in China and is an area where harmful algal blooms (HABs) have occurred frequently. In this study, differences in the phytoplankton community between microscopic observations and 18S rDNA metabarcoding were compared in 89 surface water samples collected from the southern Chinese coast and the western South China Sea (SCS). This is the first report investigating the phytoplankton community and HAB species using a combination of morphological and metabarcoding approaches in this sea area. There were substantial differences in phytoplankton community structure detected by the two methods. Microscopic observation revealed diatom predominance in the phytoplankton community, while metabarcoding indicated dinoflagellate dominance. The phytoplankton community structure obtained by microscopic observation better reflects the real situation in the water column. Metabarcoding annotated more species than morphospecies observed by microscopy. Haptophyta and Cryptophyta were the specific phyla detected in metabarcoding but were missed in microscopy due to their small size. Conversely, some taxa were found in microscopic analysis alone, such as species in Dinophysis, Prorocentrum, and Scrippsiella, suggesting some biases during metabarcoding and gaps in sequence databases. Metabarcoding is superior for detecting morphologically cryptic, small-sized and HAB taxa, such as unarmored dinoflagellates, nanosized hatophytes and chlorophytes, as well as multiple species in Alexandrium, Pseudonitzschia, and Chaetoceros in our study. A total of 62 HAB taxa were identified in this study, including blooming and potentially toxic species. Diatom abundances generally decreased southward, while those of dinoflagellates and haptophytes showed the opposite trend. Chlorophytes were mainly distributed in coastal waters, especially in the Pearl River Estuary. Phytoplankton community structures were shaped by nutrients and salinity, and phosphorus was the most limiting factor for phytoplankton growth. The phytoplankton community in the western SCS showed unique characteristics away from those in the coastal sea areas. The results suggest that the combination of morphological and metabarcoding approaches comprehensively reveals the phytoplankton community structure and diversity of HAB species.
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Affiliation(s)
- Zhaohui Wang
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Lei Liu
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Yali Tang
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Aifeng Li
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Chao Liu
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Changliang Xie
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
| | - Lijuan Xiao
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Songhui Lu
- College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
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18
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Sildever S, Nishi N, Inaba N, Asakura T, Kikuchi J, Asano Y, Kobayashi T, Gojobori T, Nagai S. Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.79471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the recent decade, high-throughput sequencing (HTS) techniques, in particular, DNA metabarcoding, have facilitated increased detection of biodiversity, including harmful algal bloom (HAB) species. In this study, the presence of HAB species and their appearance patterns were investigated by employing molecular and light microscopy-based monitoring in Tokyo Bay, Japan. The potential co-appearance patterns between the HAB species, as well as with other eukaryotes and prokaryotes were investigated using correlation and association rule-based time-series analysis. In total, 40 unique HAB species were detected, including 12 toxin-producing HAB species previously not reported from the area. More than half of the HAB species were present throughout the sampling season (summer to autumn) and no structuring or succession patterns associated with the environmental conditions could be detected. Statistically significant (p < 0.05, rS ranging from −0.88 to 0.90) associations were found amongst the HAB species and other eukaryotic and prokaryotic species, including genera containing growth-limiting bacteria. However, significant correlations between species differed amongst the years, indicating that variability in environmental conditions between the years may have a stronger influence on the microalgal community structure and interspecies interactions than the variability during the sampling season. The association rule-based time-series analysis allowed the detection of a previously reported negative relationship between Synechococcus sp. and Skeletonema sp. in nature. Overall, the results support the applicability of metabarcoding and HTS-based microalgae monitoring, as it facilitates more precise species identification compared to light microscopy, as well as provides input for investigating potential interactions amongst different species/groups through simultaneous detection of multiple species/genera.
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Santibáñez P, Romalde J, Fuentes D, Figueras A, Figueroa J. Health Status of Mytilus chilensis from Intensive Culture Areas in Chile Assessed by Molecular, Microbiological, and Histological Analyses. Pathogens 2022; 11:pathogens11050494. [PMID: 35631015 PMCID: PMC9145640 DOI: 10.3390/pathogens11050494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/30/2021] [Accepted: 01/11/2022] [Indexed: 12/04/2022] Open
Abstract
Shellfish farming is a relevant economic activity in Chile, where the inner sea in Chiloé island concentrates 99% of the production of the mussel Mytilus chilensis. This area is characterized by the presence of numerous human activities, which could harm the quality of seawater. Additionally, the presence of potentially pathogenic microorganisms can influence the health status of mussels, which must be constantly monitored. To have a clear viewpoint of the health status of M. chilensis and to study its potential as a host species for exotic diseases, microbiological, molecular, and histological analyses were performed. This study was carried out in October 2018, where M. chilensis gut were studied for: presence of food-borne bacteria (Vibrio parahaemolyticus, Escherichia coli, Salmonella spp.), exotic bacteria (“Candidatus Xenohaliotis californiensis”), viruses (abalone and Ostreid herpes virus), and protozoa (Marteilia spp., Perkinsus spp. and Bonamia spp.). Additionally, 18S rDNA metabarcoding and histology analyses were included to have a complete evaluation of the health status of M. chilensis. Overall, despite the presence of risk factors, abnormal mortality rates were not reported during the monitoring period and the histological examination did not reveal significant lesions. Pathogens of mandatory notification to World Organization for Animal Health (OIE) and the Chilean National Fisheries and Aquaculture Service (SERNAPESCA) were not detected, which confirms that M. chilensis have a good health status, highlighting the importance of an integrated vision of different disciplines to ensure the sustainability of this important mussel industry in Chile.
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Affiliation(s)
- Pablo Santibáñez
- Programa de Doctorado en Ciencias de la Acuicultura, Facultad de Ciencias, Universidad Austral de Chile, Los Pinos s/n, Balneario Pelluco, Puerto Montt 5110566, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Bío-Bío 4030000, Chile;
- Correspondence:
| | - Jesús Romalde
- Department of Microbiology and Parasitology, CRETUS & CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Derie Fuentes
- Bio-Computing and Applied Genetics Division, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago 8580704, Chile;
| | - Antonio Figueras
- Institute of Marine Research (IIM), National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain;
| | - Jaime Figueroa
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Bío-Bío 4030000, Chile;
- Department of Biochemistry and Microbiology, Faculty of Biochemistry, University Austral of Chile, Valdivia, Los Ríos 5091000, Chile
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20
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Liu S, Xu Q, Liu K, Zhao Y, Chen N. Chloroplast Genomes for Five Skeletonema Species: Comparative and Phylogenetic Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:774617. [PMID: 34966403 PMCID: PMC8710728 DOI: 10.3389/fpls.2021.774617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Skeletonema species are cosmopolitan coastal diatoms that exhibit important roles in ecological system. The chloroplast genomes (cpDNAs) have been proven to be important in the study of molecular evolution and genetic diversity. However, cpDNA of only a single Skeletonema species (S. pseudocostatum) has been constructed, hindering in-depth investigation on Skeletonema species. In this study, complete cpDNAs of five Skeletonema species were constructed with cpDNAs of four species S. marinoi, S. tropicum, S. costatum, and S. grevillea constructed for the first time. These cpDNAs had similar sizes and same numbers of genes. These cpDNAs were highly syntenic with no substantial expansions, contractions, or inversions. Interestingly, two copies of petF, which encodes ferredoxin with critical role in iron dependency, were found in all five Skeletonema species, with one copy in the cpDNA and another copy in the nuclear genome of each species. Selection analysis revealed that all PCGs of cpDNAs were undergoing purifying selection. Despite the high conservation of these cpDNAs, nine genomic regions with high sequence divergence were identified, which illustrated substantial variations that could be used as markers for phylogenetic inference and for tracking Skeletonema species in the field. Additionally, the numbers of simple sequence repeats varied among different cpDNAs, which were useful for detecting genetic polymorphisms. The divergence times estimated using PCGs of cpDNAs revealed that most of these species were established within ∼33 Mya, consistent with that estimated using mtDNAs. Overall, the current study deepened our understanding about the molecular evolution of Skeletonema cpDNAs.
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Affiliation(s)
- Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Functional Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Functional Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Functional Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yongfang Zhao
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Functional Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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21
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Liu S, Zhang M, Zhao Y, Chen N. Biodiversity and Spatial-Temporal Dynamics of Margalefidinium Species in Jiaozhou Bay, China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:11637. [PMID: 34770163 PMCID: PMC8582988 DOI: 10.3390/ijerph182111637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023]
Abstract
Many Margalefidinium species are cosmopolitan harmful algal bloom (HAB) species that have caused huge economic and ecological damage. Despite extensive research on Margalefidinium species, the biodiversity and spatial-temporal dynamics of these species remain obscure. Jiaozhou Bay is an ideal area for HAB research, being one of the earliest marine survey areas in China. In this study, we carried out the first metabarcoding study on the temporal and spatial dynamics of Margalefidinium species using the 18S rDNA V4 region as the molecular marker and samples collected monthly at 12 sampling sites in Jiaozhou Bay in 2019. Two harmful Margalefidinium species (M. polykrikoides and M. fulvescens) were identified with potentially high genetic diversity (although we cannot rule out the possibility of intra-genome sequence variations). Both M. polykrikoides and M. fulvescens demonstrated strong temporal preference with a sharp peak of abundance in early autumn (September), but without showing strong location preference in Jiaozhou Bay. Our results revealed that temperature might be the main driver for their temporal dynamics. Knowledge of biodiversity and spatial-temporal dynamics of the Margalefidinium species may shed light on the understanding of mechanisms underlying strongly biased occurrences of Margalefidinium blooms recorded globally.
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Affiliation(s)
- Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.L.); (M.Z.)
- Functional Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Mengjia Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.L.); (M.Z.)
- Functional Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China;
| | - Yongfang Zhao
- College of Marine Science, University of Chinese Academy of Sciences, Beijing 100039, China;
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.L.); (M.Z.)
- Functional Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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22
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Metabarcoding Analysis of Harmful Algal Bloom Species in the Western Pacific Seamount Regions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111470. [PMID: 34769984 PMCID: PMC8582749 DOI: 10.3390/ijerph182111470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022]
Abstract
The Western Pacific is the most oligotrophic sea on Earth, with numerous seamounts. However, the plankton diversity and biogeography of the Western Pacific in general and the seamount regions in particular remains largely unexplored. In this project, we quantitatively analyzed the composition and distribution patterns of plankton species in the Western Pacific seamount regions by applying metabarcoding analysis. We identified 4601 amplicon sequence variants (ASVs) representing 34 classes in seven protist phyla/divisions in the Western Pacific seamount regions, among which Dinoflagellata was by far the most dominant division. Among the 336 annotated phytoplankton species (including species in Dinoflagellata), we identified 36 harmful algal bloom (HAB) species, many of which displayed unique spatial distribution patterns in the Western Pacific seamount regions. This study was the first attempt in applying ASV-based metabarcoding analysis in studying phytoplankton and HAB species in the Western Pacific seamount regions, which may facilitate further research on the potential correlation between HABs in the Western Pacific seamount regions and coastal regions.
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Liu S, Wang Y, Xu Q, Zhang M, Chen N. Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation. BMC Genomics 2021; 22:746. [PMID: 34654361 PMCID: PMC8520197 DOI: 10.1186/s12864-021-07999-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Background Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as “super barcode” in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi. Results In this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya. Conclusions The availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07999-z.
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Affiliation(s)
- Shuya Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yichao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Qing Xu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjia Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Nansheng Chen
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China. .,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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24
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Chen Y, Xu Q, Gibson K, Chen N. Metabarcoding dissection of harmful algal bloom species in the East China Sea off Southern Zhejiang Province in late spring. MARINE POLLUTION BULLETIN 2021; 169:112586. [PMID: 34116370 DOI: 10.1016/j.marpolbul.2021.112586] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 06/12/2023]
Abstract
The coastal region of the East China Sea (ECS) is a famous "hotspot" for harmful algal blooms (HABs) in China. We hypothesize that such frequent occurrences of diverse HABs in the ECS are determined by the presence of unique HAB species in this region. In this project, we identified 3966 amplicon sequence variants (ASVs) representing 35 classes in six protist phyla/divisions. Among the 237 annotated protist species, we identified 58 HAB species, of which 23 HAB species had never been previously reported in the ECS. Many HAB species also displayed unique spatial distribution patterns in the ECS. Notably, we identified three HAB species Prorocentrum donghaiense, Lebouridinium glaucum and Noctiluca scintillans in the site S05-1 with substantially elevated abundance, suggesting that this sampling site was experiencing a multiple-species HAB event. This study was the first attempt in applying ASV-based metabarcoding analysis in studying protist and HAB species in the ECS.
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Affiliation(s)
- Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; University of Chinese Academy of Sciences, Beijing 10039, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
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25
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Wang X, Song H, Wang Y, Chen N. Research on the biology and ecology of the harmful algal bloom species Phaeocystis globosa in China: Progresses in the last 20 years. HARMFUL ALGAE 2021; 107:102057. [PMID: 34456018 DOI: 10.1016/j.hal.2021.102057] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/09/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Chinese researchers have made substantial progresses in research on the harmful algal bloom (HAB) species Phaeocystis globosa since the first P. globosa bloom outbreak in the Chinese coastal waters in 1997. However, as many results, especially the earlier ones, were published in non-English literature, much of the research on P. globosa biology, ecology, and biogeochemistry made by Chinese researchers have been unknown to colleagues from other countries. We review current knowledge on taxonomy, morphology, genetics, physiology, survival strategies and mitigation of P. globosa gained by Chinese researchers from the past two decades. P. globosa is the only Phaeocystis species that causes blooms in the Chinese waters, although other Phaeocystis species including P. jahnii and P. cordata have been detected in Chinese coastal regions. P. globosa has a complex life history with at least two morphotypes including a haploid flagellate and a diploid colonial cell. Colonial P. globosa blooms typically occur in winter after a diatom bloom in coastal waters of the South China Sea. P. globosa in Chinese coastal waters usually has extremely large colonial sizes, up to 3 cm in diameter, an order of magnitude greater than that observed in European coastal waters. The development of giant colonies is associated with enhanced sinking rate, limited nutrient diffusion, as well as decreased stability of colonies. The Chinese P. globosa strains also showed strong genetic diversity and physiological plasticity, being able to grow and develop into colonies at higher temperature and irradiance relative to that in European waters. High genetic diversity of P. globosa was revealed by developing high-resolution and high-specificity molecular markers including Phaeocystis globosa chloroplast 1 (pgcp1). Due to the severe impact of P. globosa on ecology and economy, much effort has been made to mitigate P. globosa blooms including the application of modified clays. Overall, P. globosa in the Chinese waters demonstrate unique genetic, phenotypical and physiological features that differ from P. globosa in other ocean regions. Further studies are needed to explore how environmental factors trigger the occurrence of P. globosa blooms and ascertain the impact of P. globosa blooms on the environment.
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Affiliation(s)
- Xiaodong Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yan Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby V5A 1S6, British Columbia, Canada.
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26
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Huang H, Xu Q, Gibson K, Chen Y, Chen N. Molecular characterization of harmful algal blooms in the Bohai Sea using metabarcoding analysis. HARMFUL ALGAE 2021; 106:102066. [PMID: 34154783 DOI: 10.1016/j.hal.2021.102066] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Although the occurrences of harmful algal blooms (HABs) have been intensifying, many HABs in coastal waters may have been neglected despite their damaging impact directly on ecology and indirectly on human and animal health. The current detection of HABs depends primarily on the water coloration, chlorophyll intensity, cell density, and mortality due to HAB toxicity. Such methods may not be adequately sensitive to detecting HABs that are relatively transient or small scale. The Bohai Sea is the largest inlet of the Yellow Sea located on the northeast coast of China and famous for shipping and marine aquacultures. HABs frequently occur in the Bohai Sea. In this study, we explored the composition, diversity, and distribution of HAB species using the metabarcoding approach. Through sequencing and the analyzing the 18S rDNA V4 region of 15 samples collected from spatially isolated sites in the Bohai Sea during an expedition in the summer of 2019, we identified 74 potential HAB species including 34 that had not been reported in the Bohai Sea in previous studies. This project provided a detailed analysis of phytoplankton composition, and molecular detection of HAB species in the Bohai Sea. In particular, these analyses revealed extremely high relative abundances of the ichthyotoxic phytoplankton species Vicicitus globosus (Dictyochophyceae) at multiple adjacent sampling sites in the Bohai Bay, which were close to the Yellow River Estuary during the expedition. The results revealed the occurrence of a potential HAB event that would be otherwise undetected using conventional methods, highlighting the sensitivity and power of metabarcoding analysis in detecting HABs and HAB species. This research suggested the value for routine and long-term monitoring of HAB species as an approach for monitoring HABs.
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Affiliation(s)
- Hailong Huang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266200, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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27
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Fu Z, Piumsomboon A, Punnarak P, Uttayarnmanee P, Leaw CP, Lim PT, Wang A, Gu H. Diversity and distribution of harmful microalgae in the Gulf of Thailand assessed by DNA metabarcoding. HARMFUL ALGAE 2021; 106:102063. [PMID: 34154784 DOI: 10.1016/j.hal.2021.102063] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Information on the diversity and distribution of harmful microalgae in the Gulf of Thailand is very limited and mainly based on microscopic observations. Here, we collected 44 water samples from the Gulf of Thailand and its adjacent water (Perhentian Island, Malaysia) for comparison in 2018. DNA metabarcoding was performed targeting the partial large subunit ribosomal RNA gene (LSU rDNA D1-D3) and the internal transcribed spacers (ITS1 and ITS2). A total of 50 dinoflagellate genera (made up of 72 species) were identified based on the LSU rDNA dataset, while the results of ITS1 and ITS2 datasets revealed 33 and 32 dinoflagellate genera comprising 69 and 64 species, respectively. Five potentially toxic Pseudo-nitzschia (Bacillariophyceae) species were detected, with four as newly recorded species in the water (Pseudo-nitzschia americana/brasilliana, Pseudo-nitzschia simulans/delicatissima, P. galaxiae and P. multistriata). The highest relative abundances of P. galaxiae and P. multistriata were found in Trat Bay and Chumphon (accounting for 0.20% and 0.06% of total ASVs abundance, respectively). Three paralytic shellfish toxin producing dinoflagellate species were detected: Alexandrium tamiyavanichii, Alexandrium fragae, and Gymnodinium catenatum. The highest abundance of A. tamiyavanichii was found in the surface sample of Chumphon (CHO7 station), accounting for 1.95% of total ASVs abundance. Two azaspiracid producing dinoflagellate species, Azadinium poporum ribotype B, Azadinium spinosum ribotype A, and a pinnatoxin producing dinoflagellate species Vulcanodinium rugosum, with two ribotypes B and C, were revealed from the datasets although with very low abundances. Six fish killing dinoflagellate species, including Margalefidinium polykrikoides group IV, Margalefidinium fulvescens, Karenia mikimotoi, Karenia selliformis ribotype B, Karlodinium australe, and Karlodinium digitatum were detected and all representing new records in this area. The findings of numerous harmful microalgal species in the Gulf of Thailand highlight the potential risk of human intoxication and fish killing events.
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Affiliation(s)
- Zhengxu Fu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | | | - Porntep Punnarak
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok 10330, Thailand
| | - Praderm Uttayarnmanee
- Marine and Coastal Resources Research and Development Center, Central Gulf of Thailand, Department of Marine and Coastal Resources, Chumphon 86000, Thailand
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Aijun Wang
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Haifeng Gu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China.
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28
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Zhang M, Cui Z, Liu F, Chen N. Definition of a High-Resolution Molecular Marker for Tracking the Genetic Diversity of the Harmful Algal Species Eucampia zodiacus Through Comparative Analysis of Mitochondrial Genomes. Front Microbiol 2021; 12:631144. [PMID: 33841358 PMCID: PMC8024477 DOI: 10.3389/fmicb.2021.631144] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
The cosmopolitan phytoplankton species Eucampia zodiacus is a common harmful algal bloom (HAB) species that have been found to cause HABs in essentially all coastal regions except the Polar regions. However, molecular information for this HAB species is limited with only a few molecular markers. In this project, we constructed the mitochondrial genome (mtDNA) of E. zodiacus, which was also the first mtDNA constructed for any species in the order Hemiaulales that includes 145 reported species (including two additional HAB species Cerataulina bicornis and Cerataulina pelagica). Comparative analysis of eight E. zodiacus strains revealed that they could not be distinguished using common molecular markers, suggesting that common molecular markers do not have adequate resolution for distinguishing E. zodiacus strains. However, these E. zodiacus strains could be distinguished using whole mtDNAs, suggesting the presence of different genotypes due to evolutionary divergence. Through comparative analysis of the mtDNAs of multiple E. zodiacus strains, we identified a new molecular marker ezmt1 that could adequately distinguish different E. zodiacus strains isolated in various coastal regions in China. This molecular marker ezmt1, which was ∼400 bp in size, could be applied to identify causative genotypes during E. zodiacus HABs through tracking the dynamic changes of genetic diversity of E. zodiacus in HABs.
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Affiliation(s)
- Mengjia Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Oceanology, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zongmei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Oceanology, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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29
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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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30
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Durán-Vinet B, Araya-Castro K, Chao TC, Wood SA, Gallardo V, Godoy K, Abanto M. Potential applications of CRISPR/Cas for next-generation biomonitoring of harmful algae blooms: A review. HARMFUL ALGAE 2021; 103:102027. [PMID: 33980455 DOI: 10.1016/j.hal.2021.102027] [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: 12/10/2020] [Revised: 03/01/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Research on harmful algal and cyanobacterial blooms (HABs and CHABs) has risen dramatically due to their increasing global distribution, frequency, and intensity. These blooms jeopardize public health, ecosystem function, sustainability and can have negative economic impacts. Numerous monitoring programs have been established using light microscopy, liquid chromatography coupled to mass spectrometry (LC-MS), ELISA, and spectrophotometry to monitor HABs/CHABs outbreaks. Recently, DNA/RNA-based molecular methods have been integrated into these programs to replace or complement traditional methods through analyzing environmental DNA and RNA (eDNA/eRNA) with techniques such as quantitative polymerase chain reaction (qPCR), fluorescent in situ hybridization (FISH), sandwich hybridization assay (SHA), isothermal amplification methods, and microarrays. These have enabled the detection of rare or cryptic species, enhanced sample throughput, and reduced costs and the need for visual taxonomic expertise. However, these methods have limitations, such as the need for high capital investment in equipment or detection uncertainties, including determining whether organisms are viable. In this review, we discuss the potential of newly developed molecular diagnosis technology based on Clustered Regularly Interspaced Short Palindromic Repeats/Cas proteins (CRISPR/Cas), which utilizes the prokaryotic adaptative immune systems of bacteria and archaea. Cas12 and Cas13-based platforms can detect both DNA and RNA with attomolar sensitivity within an hour. CRISPR/Cas diagnostic is a rapid, inexpensive, specific, and ultrasensitive technology that, with some further development, will provide many new platforms that can be used for HABs/CHABs biomonitoring and research.
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Affiliation(s)
- B Durán-Vinet
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile; Bachelor of Biotechnology (Honours) Program, Faculty of Agricultural and Forestry Sciences, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile.
| | - K Araya-Castro
- Doctoral Program in Science of Natural Resources, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - T C Chao
- Institute of Environmental Change & Society, Department of Biology, University of Regina, Wascana Parkway, 3737 Regina, Canada
| | - S A Wood
- Coastal and Freshwater Group, Cawthron Institute, 98 Halifax Street East, Nelson 7010, New Zealand
| | - V Gallardo
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile; Bachelor of Biotechnology (Honours) Program, Faculty of Agricultural and Forestry Sciences, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - K Godoy
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Microscopy and Flow Cytometry Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
| | - M Abanto
- Scientific and Technological Bioresource Nucleus (BIOREN-UFRO), Genomics and Bioinformatics Unit, Universidad de La Frontera, Av. Francisco Salazar, 1145 Temuco, Chile
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31
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Esenkulova S, Sutherland BJ, Tabata A, Haigh N, Pearce CM, Miller KM. Comparing metabarcoding and morphological approaches to identify phytoplankton taxa associated with harmful algal blooms. Facets (Ott) 2020. [DOI: 10.1139/facets-2020-0025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Molecular techniques are expected to be highly useful in detecting taxa causing harmful algal blooms (HABs). This is the first report in Canada evaluating HABs-related species identification using a combination of morphological and molecular approaches. Microscopy, quantitative polymerase chain reaction (qPCR), and metabarcoding with multiple markers (i.e., 16S, 18S-dinoflagellate and 18S-diatom, large subunit (28S) rDNA) were applied on samples ( n = 54) containing suspected harmful algae (e.g., Alexandrium spp., Chattonella sp., Chrysochromulina spp., Dictyocha spp., Heterosigma akashiwo, Protoceratium reticulatum, Pseudochattonella verruculosa, Pseudo-nitzschia spp., Pseudopedinella sp.). Owing to methodology limitations, qPCR result interpretation was limited, although good detectability occurred using previously published assays for Alexandrium tamarense, H. akashiwo, and P. verruculosa. Overall, the multiple-marker metabarcoding results were superior to the morphology-based methods, with the exception of taxa from the silicoflagellate group. The combined results using both 18S markers and the 28S marker together closely corresponded with morphological identification of targeted species, providing the best overall taxonomic coverage and resolution. The most numerous unique taxa were identified using the 18S-dinoflagellate amplicon, and the best resolution to the species level occurred using the 28S amplicon. Molecular techniques are therefore promising for HABs taxa detection but currently depend on deploying multiple markers for metabarcoding.
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Affiliation(s)
- Svetlana Esenkulova
- Pacific Salmon Foundation, #300 1682 West 7th Avenue, Vancouver, BC V6J 4S6, Canada
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Ben J.G. Sutherland
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Amy Tabata
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Nicola Haigh
- Microthalassia Inc., Nanaimo, BC V9T 1T4, Canada
| | - Christopher M. Pearce
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
| | - Kristina M. Miller
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC V9T 6N7, Canada
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