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Wang Y, Zhu Y, Wang K, Tan Y, Bing X, Jiang J, Fang W, Chen L, Liao H. Principles and research progress of physical prevention and control technologies for algae in eutrophic water. iScience 2024; 27:109990. [PMID: 38840838 PMCID: PMC11152667 DOI: 10.1016/j.isci.2024.109990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
The abnormal reproduction of algae in water worldwide is prominent in the context of human interference and global climate change. This study first thoroughly analyzed the effects of physical factors, such as light, temperature, hydrodynamics, and operational strategies, on algal growth and their mechanisms. Physical control techniques are safe and have great potential for preventing abnormal algal blooms in the absence of chemical reagents. The focus was on the principles and possible engineering applications of physical shading, ultrasound, micro-current, and ultraviolet (UV) technologies, in controlling abnormal algal reproduction. Physical shading can inhibit or weaken photosynthesis in algae, thereby inhibiting their growth. Ultrasound mainly affects the physiological and biochemical activities of cells by destroying the cell walls, air cells, and active enzymes. Micro-currents destroy the algal cell structure through direct and indirect oxidation, leading to algal cell death. UV irradiation can damage DNA, causing organisms to be unable to reproduce or algal cells to die directly. This article comprehensively summarizes and analyzes the advantages of physical prevention and control technologies for the abnormal reproduction of algae, providing a scientific basis for future research. In the future, attempts will be made toward appropriately and comprehensively utilizing various physical technologies to control algal blooms. The establishment of an intelligent, comprehensive physical prevention and control system to achieve environmentally friendly, economical, and effective physical prevention and control of algae, such as the South-to-North Water Diversion Project in China, is of great importance for specific waters.
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Affiliation(s)
- Yuyao Wang
- State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou 730070, China
| | - Yuanrong Zhu
- State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Kuo Wang
- State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yidan Tan
- State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xiaojie Bing
- State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Juan Jiang
- State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
- College of Environment, Hohai University, Nanjing 210098, China
| | - Wen Fang
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou 730070, China
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Chen
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China
| | - Haiqing Liao
- State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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2
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Wang J, Curson ARJ, Zhou S, Carrión O, Liu J, Vieira AR, Walsham KS, Monaco S, Li CY, Dong QY, Wang Y, Rivera PPL, Wang XD, Zhang M, Hanwell L, Wallace M, Zhu XY, Leão PN, Lea-Smith DJ, Zhang YZ, Zhang XH, Todd JD. Alternative dimethylsulfoniopropionate biosynthesis enzymes in diverse and abundant microorganisms. Nat Microbiol 2024:10.1038/s41564-024-01715-9. [PMID: 38862603 DOI: 10.1038/s41564-024-01715-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/29/2024] [Indexed: 06/13/2024]
Abstract
Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound with roles in stress protection, chemotaxis, nutrient and sulfur cycling and climate regulation. Here we report the discovery of a bifunctional DMSP biosynthesis enzyme, DsyGD, in the transamination pathway of the rhizobacterium Gynuella sunshinyii and some filamentous cyanobacteria not previously known to produce DMSP. DsyGD produces DMSP through its N-terminal DsyG methylthiohydroxybutyrate S-methyltransferase and C-terminal DsyD dimethylsulfoniohydroxybutyrate decarboxylase domains. Phylogenetically distinct DsyG-like proteins, termed DSYE, with methylthiohydroxybutyrate S-methyltransferase activity were found in diverse and environmentally abundant algae, comprising a mix of low, high and previously unknown DMSP producers. Algae containing DSYE, particularly bloom-forming Pelagophyceae species, were globally more abundant DMSP producers than those with previously described DMSP synthesis genes. This work greatly increases the number and diversity of predicted DMSP-producing organisms and highlights the importance of Pelagophyceae and other DSYE-containing algae in global DMSP production and sulfur cycling.
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Affiliation(s)
- Jinyan Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Shun Zhou
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ornella Carrión
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ji Liu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Ana R Vieira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal
| | - Keanu S Walsham
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Chun-Yang Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qing-Yu Dong
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yu Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peter Paolo L Rivera
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao-Di Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Min Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Libby Hanwell
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Wallace
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Xiao-Yu Zhu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Pedro N Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Matosinhos, Portugal
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yu-Zhong Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, China.
| | - Jonathan D Todd
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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3
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Wang H, Wu P, Xiong L, Kim HS, Kim JH, Ki JS. Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms. Eur J Protistol 2024; 93:126061. [PMID: 38394997 DOI: 10.1016/j.ejop.2024.126061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.
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Affiliation(s)
- Hui Wang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea
| | - Peiling Wu
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Lu Xiong
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Han-Sol Kim
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea
| | - Jin Ho Kim
- Department of Earth and Marine Science, College of Ocean Sciences, Jeju National University, Jeju 63243, Republic of Korea
| | - Jang-Seu Ki
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea; Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea.
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4
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Dawydiak W, Gobler CJ. Transcription of biochemical defenses by the harmful brown tide pelagophyte, Aureococcus anophagefferens, in response to the protozoan grazer, Oxyrrhis marina. Front Microbiol 2023; 14:1295160. [PMID: 38163083 PMCID: PMC10756674 DOI: 10.3389/fmicb.2023.1295160] [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: 09/15/2023] [Accepted: 11/06/2023] [Indexed: 01/03/2024] Open
Abstract
Aureococcus anophagefferens is a small marine pelagophyte that forms recurrent harmful brown tides blooms with adverse ecological and economic impacts. During blooms, A. anophagefferens experiences lower zooplankton grazing mortality than other phytoplankton potentially due to the synthesis of anti-predator compounds including extracellular polysaccharides. This study characterized the transcriptomic response of A. anophagefferens when exposed to the protozooplankton, Oxyrrhis marina, and assessed whether this response involved chemical cues. Transcriptomes were generated from A. anophagefferens populations grown at high (1×106 cells mL-1) and low (5×105 cells mL-1) cell densities incubated directly with O. marina or receiving only filtrate from co-cultures of A. anophagefferens and O. marina to evaluate the role of chemical cues. There were a greater number of genes differentially expressed in response to grazing in the lower concentration of A. anophagefferens compared to the high concentration treatment and in response to direct grazing compared to filtrate. KEGG pathway analysis revealed that direct grazer exposure led to a significant increase in transcripts of genes encoding secondary metabolite production (p < 0.001). There was broad transcriptional evidence indicating the induction of biosynthetic pathways for polyketides and sterols in response to zooplankton grazers, compounds associated with damage to marine organisms. In addition, exposure to O. marina elicited changes in the abundance of transcripts associated with carbohydrate metabolism that could support the formation of an extracellular polysaccharide matrix including genes related to glycoprotein synthesis and carbohydrate transport. Collectively, these findings support the hypothesis that A. anophagefferens can induce biochemical pathways that reduce grazing mortality and support blooms.
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Affiliation(s)
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
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5
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Truchon AR, Chase EE, Gann ER, Moniruzzaman M, Creasey BA, Aylward FO, Xiao C, Gobler CJ, Wilhelm SW. Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research. Front Microbiol 2023; 14:1284617. [PMID: 38098665 PMCID: PMC10720644 DOI: 10.3389/fmicb.2023.1284617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/30/2023] [Indexed: 12/17/2023] Open
Abstract
Since the discovery of the first "giant virus," particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales. Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense. Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions.
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Affiliation(s)
- Alexander R Truchon
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Emily E Chase
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Eric R Gann
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States
- Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
- Surgical Critical Care Initiative (SC2i), Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, University of Miami, Miami, FL, United States
| | - Brooke A Creasey
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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6
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Ajani PA, Savela H, Kahlke T, Harrison D, Jeffries T, Kohli GS, Verma A, Laczka O, Doblin MA, Seymour JR, Larsson ME, Potts J, Scanes P, Gribben PE, Harrison L, Murray SA. Response of planktonic microbial assemblages to disturbance in an urban sub-tropical estuary. WATER RESEARCH 2023; 243:120371. [PMID: 37506634 DOI: 10.1016/j.watres.2023.120371] [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: 02/14/2023] [Revised: 06/26/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023]
Abstract
Microbes are sensitive indicators of estuarine processes because they respond rapidly to dynamic disturbance events. As most of the world's population lives in urban areas and climate change-related disturbance events are becoming more frequent, estuaries bounded by cities are experiencing increasing stressors, at the same time that their ecosystem services are required more than ever. Here, using a multidisciplinary approach, we determined the response of planktonic microbial assemblages in response to seasonality and a rainfall disturbance in an urban estuary bounded by Australia's largest city, Sydney. We used molecular barcoding (16S, 18S V4 rRNA) and microscopy-based identification to compare microbial assemblages at locations with differing characteristics and urbanisation histories. Across 142 samples, we identified 8,496 unique free-living bacterial zOTUs, 8,175 unique particle associated bacterial zOTUs, and 1,920 unique microbial eukaryotic zOTUs. Using microscopy, we identified only the top <10% abundant, larger eukaryotic taxa (>10 µm), however quantification was possible. The site with the greater history of anthropogenic impact showed a more even community of associated bacteria and eukaryotes, and a significant increase in dissolved inorganic nitrogen following rainfall, when compared to the more buffered site. This coincided with a reduced proportional abundance of Actinomarina and Synechococcus spp., a change in SAR 11 clades, and an increase in the eukaryotic microbial groups Dinophyceae, Mediophyceae and Bathyoccocaceae, including a temporary dominance of the harmful algal bloom dinoflagellate Prorocentrum cordatum (syn. P. minimum). Finally, a validated hydrodynamic model of the estuary supported these results, showing that the more highly urbanised and upstream location consistently experienced a higher magnitude of salinity reduction in response to rainfall events during the study period. The best abiotic variables to explain community dissimilarities between locations were TDP, PN, modelled temperature and salinity (r = 0.73) for the free living bacteria, TP for the associated bacteria (r = 0.43), and modelled temperature (r = 0.28) for the microbial eukaryotic communities. Overall, these results show that a minor disturbance such as a brief rainfall event can significantly shift the microbial assemblage of an anthropogenically impacted area within an urban estuary to a greater degree than a seasonal change, but may result in a lesser response to the same disturbance at a buffered, more oceanic influenced location. Fine scale research into the factors driving the response of microbial communities in urban estuaries to climate related disturbances will be necessary to understand and implement changes to maintain future estuarine ecosystem services.
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Affiliation(s)
- Penelope A Ajani
- University of Technology Sydney, School of Life Sciences, 15 Broadway, Ultimo NSW 2007, Australia; Sydney Institute of Marine Sciences, Mosman, New South Wales 2088, Australia.
| | - Henna Savela
- University of Technology Sydney, School of Life Sciences, 15 Broadway, Ultimo NSW 2007, Australia
| | - Tim Kahlke
- University of Technology Sydney, School of Life Sciences, 15 Broadway, Ultimo NSW 2007, Australia; University of Technology Sydney, Climate Change Cluster, 15 Broadway, Ultimo NSW 2007, Australia
| | - Daniel Harrison
- National Marine Science Centre, Southern Cross University, 2 Bay Drive, Coffs Harbour NSW 2450, Australia
| | - Thomas Jeffries
- Western Sydney University, School of Science, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Gurjeet S Kohli
- University of Technology Sydney, Climate Change Cluster, 15 Broadway, Ultimo NSW 2007, Australia
| | - Arjun Verma
- University of Technology Sydney, School of Life Sciences, 15 Broadway, Ultimo NSW 2007, Australia; University of Technology Sydney, Climate Change Cluster, 15 Broadway, Ultimo NSW 2007, Australia
| | - Olivier Laczka
- University of Technology Sydney, Climate Change Cluster, 15 Broadway, Ultimo NSW 2007, Australia
| | - Martina A Doblin
- Sydney Institute of Marine Sciences, Mosman, New South Wales 2088, Australia; University of Technology Sydney, Climate Change Cluster, 15 Broadway, Ultimo NSW 2007, Australia
| | - Justin R Seymour
- University of Technology Sydney, Climate Change Cluster, 15 Broadway, Ultimo NSW 2007, Australia
| | - Michaela E Larsson
- University of Technology Sydney, Climate Change Cluster, 15 Broadway, Ultimo NSW 2007, Australia
| | - Jaimie Potts
- Science, Economics and Insights Division, NSW Department of Planning and Environment
| | - Peter Scanes
- Science, Economics and Insights Division, NSW Department of Planning and Environment
| | - Paul E Gribben
- Sydney Institute of Marine Sciences, Mosman, New South Wales 2088, Australia; University of NSW, Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, New South Wales 2052, Australia
| | - Luke Harrison
- Marine Studies Institute, School of Geosciences, University of Sydney, Australia
| | - Shauna A Murray
- University of Technology Sydney, School of Life Sciences, 15 Broadway, Ultimo NSW 2007, Australia; Sydney Institute of Marine Sciences, Mosman, New South Wales 2088, Australia
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7
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Davison JR, Rajwani R, Zhao G, Bewley CA. The genome of antibiotic-producing colonies of the Pelagophyte alga Chrysophaeum taylorii reveals a diverse and non-canonical capacity for secondary metabolism. Sci Rep 2023; 13:11944. [PMID: 37488207 PMCID: PMC10366177 DOI: 10.1038/s41598-023-38042-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/01/2023] [Indexed: 07/26/2023] Open
Abstract
Chrysophaeum taylorii is a member of an understudied clade of marine algae that can be responsible for harmful coastal blooms and is known to accumulate bioactive natural products including antibiotics of the chrysophaentin class. Whole genome sequencing of laboratory-cultivated samples revealed an extensive and diverse complement of secondary metabolite biosynthetic genes in C. taylorii, alongside a small microbiome with a more limited biosynthetic potential. 16S microbiome analysis of laboratory cultured alongside wild-collected samples revealed several common taxa; however, analysis of biosynthetic genes suggested an algal origin for the chrysophaentins, possibly via one of several non-canonical polyketide synthase genes encoded within the genome.
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Affiliation(s)
- Jack R Davison
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA.
- LifeMine Therapeutics, 30 Acorn Park Dr., Cambridge, MA, 02140, USA.
| | - Rahim Rajwani
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA
| | - Gengxiang Zhao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Mailstop 0820, Bethesda, MD, 20892, USA.
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Ban H, Sato S, Yoshikawa S, Yamada K, Nakamura Y, Ichinomiya M, Sato N, Blanc-Mathieu R, Endo H, Kuwata A, Ogata H. Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs. Commun Biol 2023; 6:697. [PMID: 37420035 PMCID: PMC10328945 DOI: 10.1038/s42003-023-05002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/31/2023] [Indexed: 07/09/2023] Open
Abstract
The order Parmales (class Bolidophyceae) is a minor group of pico-sized eukaryotic marine phytoplankton that contains species with cells surrounded by silica plates. Previous studies revealed that Parmales is a member of ochrophytes and sister to diatoms (phylum Bacillariophyta), the most successful phytoplankton group in the modern ocean. Therefore, parmalean genomes can serve as a reference to elucidate both the evolutionary events that differentiated these two lineages and the genomic basis for the ecological success of diatoms vs. the more cryptic lifestyle of parmaleans. Here, we compare the genomes of eight parmaleans and five diatoms to explore their physiological and evolutionary differences. Parmaleans are predicted to be phago-mixotrophs. By contrast, diatoms have lost genes related to phagocytosis, indicating the ecological specialization from phago-mixotrophy to photoautotrophy in their early evolution. Furthermore, diatoms show significant enrichment in gene sets involved in nutrient uptake and metabolism, including iron and silica, in comparison with parmaleans. Overall, our results suggest a strong evolutionary link between the loss of phago-mixotrophy and specialization to a silicified photoautotrophic life stage early in diatom evolution after diverging from the Parmales lineage.
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Affiliation(s)
- Hiroki Ban
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Shinya Sato
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Shinya Yoshikawa
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Kazumasa Yamada
- Department of Marine Science and Technology, Fukui Prefectural University, 1-1 Gakuen-cho, Obama City, Fukui, 917-0003, Japan
| | - Yoji Nakamura
- Bioinformatics and Biosciences Division, Fisheries Stock Assessment Center, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan
| | - Mutsuo Ichinomiya
- Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto, 862-8502, Japan
| | - Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Akira Kuwata
- Shiogama field station, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, 3-27-5 Shinhama-cho, Shiogama, Miyagi, Japan.
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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9
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Chen Y, Chen T, Duan W, Liu J, Si Y, Dong Z. Rapid measurement of brown tide algae using Zernike moments and ensemble learning based on excitation-emission matrix fluorescence. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 294:122547. [PMID: 36870184 DOI: 10.1016/j.saa.2023.122547] [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: 08/26/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Accurate real-time prediction of microalgae density has great practical significance for taking countermeasures before the advent of Harmful algal blooms (HABs), and the non-destructive and sensitive property of excitation-emission matrix fluorescence (EEMF) spectroscopy makes it applicable to online monitoring and control. In this study, an efficient image preprocessing algorithm based on Zernike moments (ZMs) was proposed to extract compelling features from EEM intensities images. The determination of the highest order of ZMs considered both reconstruction error and computational cost, then the optimal subset of preliminarily extracted 36 ZMs was screened via the BorutaShap algorithm. Aureococcus anophagefferens concentration prediction models were developed by combining BorutaShap and ensemble learning models (random forest (RF), gradient boosting decision tree (GBDT), and XGBoost). The experimental results show that BorutaShap_GBDT preserved the superior subset of ZMs, and the integration of BorutaShap_GBDT and XGBoost achieved the highest prediction accuracy. This research provides a new and promising strategy for rapidly measuring microalgae cell density.
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Affiliation(s)
- Ying Chen
- Hebei Province Key Laboratory of Test/Measurement Technology and Instrument, School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, China.
| | - Ting Chen
- Hebei Province Key Laboratory of Test/Measurement Technology and Instrument, School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, China
| | - Weiliang Duan
- Hebei Province Key Laboratory of Test/Measurement Technology and Instrument, School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, China
| | - Junfei Liu
- Hebei Province Key Laboratory of Test/Measurement Technology and Instrument, School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, China
| | - Yu Si
- Hebei Province Key Laboratory of Test/Measurement Technology and Instrument, School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, China
| | - Zhiyang Dong
- Hebei Province Key Laboratory of Test/Measurement Technology and Instrument, School of Electrical Engineering, Yanshan University, Qinhuangdao, Hebei 066004, China
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10
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Kato Y, Inabe K, Haraguchi Y, Shimizu T, Kondo A, Hasunuma T. L-Lactate treatment by photosynthetic cyanobacteria expressing heterogeneous L-lactate dehydrogenase. Sci Rep 2023; 13:7249. [PMID: 37142758 PMCID: PMC10160077 DOI: 10.1038/s41598-023-34289-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023] Open
Abstract
L-Lactate is a major waste compound in cultured animal cells. To develop a sustainable animal cell culture system, we aimed to study the consumption of L-lactate using a photosynthetic microorganism. As genes involved in L-lactate utilization were not found in most cyanobacteria and microalgae, we introduced the NAD-independent L-lactate dehydrogenase gene from Escherichia coli (lldD) into Synechococcus sp. PCC 7002. The lldD-expressing strain consumed L-lactate added to basal medium. This consumption was accelerated by expression of a lactate permease gene from E. coli (lldP) and an increase in culture temperature. Intracellular levels of acetyl-CoA, citrate, 2-oxoglutarate, succinate, and malate, and extracellular levels of 2-oxoglutarate, succinate, and malate, increased during L-lactate utilization, suggesting that the metabolic flux from L-lactate was distributed toward the tricarboxylic acid cycle. This study provides a perspective on L-lactate treatment by photosynthetic microorganisms, which would increase the feasibility of animal cell culture industries.
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Affiliation(s)
- Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kosuke Inabe
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Yuji Haraguchi
- Institute of Advanced Biomedical Engineering and Science, TWIns, Tokyo Women's Medical University, 8-1 Kawada, Shinjuku, Tokyo, 162-8666, Japan
| | - Tatsuya Shimizu
- Institute of Advanced Biomedical Engineering and Science, TWIns, Tokyo Women's Medical University, 8-1 Kawada, Shinjuku, Tokyo, 162-8666, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
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11
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Cheng HM, Zhang SF, Ning XL, Peng JX, Li DX, Zhang H, Zhang K, Lin L, Liu SQ, Smith WO, Wang DZ. Elucidating colony bloom formation mechanism of a harmful alga Phaeocystis globosa (Prymnesiophyceae) using metaproteomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161846. [PMID: 36709898 DOI: 10.1016/j.scitotenv.2023.161846] [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: 10/25/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Phaeocystis is a globally distributed Prymnesiophyte genus and usually forms massive harmful colony blooms, which impact marine ecosystem, mariculture, human health, and even threaten coastal nuclear power plant safety. However, the mechanisms behind the colony formation from the solitary cells remain poorly understood. Here, we investigated metabolic processes of both solitary and non-flagellated colonial cells of Phaeocystis globosa at different colony bloom stages in the subtropical Beibu Gulf using a metaproteomic approach. Temperature was significantly correlated with Phaeocystis colony bloom formation, and the flagellated motile solitary cells with abundant flagellum-associated proteins, such as tubulin and dynein, were the exclusive cellular morphotype at the solitary cell stage featured with temperatures ≥21 °C. When the temperature decreased to <21 °C, tiny colonies appeared and the flagellum-associated proteins were down-regulated in both solitary and non-flagellated colonial cells, while proteins involved in biosynthesis, chain polymerization and aggregation of glycosaminoglycan (GAG), a key constituent of gelatinous matrix, were up-regulated, indicating the central role of active GAG biosynthesis during the colony formation. Furthermore, light utilization, carbon fixation, nitrogen assimilation, and amino acid and protein synthesis were also enhanced to provide sufficient energy and substrates for GAG biosynthesis. This study highlighted that temperature induced re-allocation of energy and substances toward GAG biosynthesis is essential for colony bloom formation of P. globosa.
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Affiliation(s)
- Hua-Min Cheng
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Xiao-Lian Ning
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Jian-Xiang Peng
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Kun Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China
| | - Si-Qi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Walker O Smith
- School of Oceanography, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200300, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361005, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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12
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Wang H, Bouwman AF, Van Gils J, Vilmin L, Beusen AHW, Wang J, Liu X, Yu Z, Ran X. Hindcasting harmful algal bloom risk due to land-based nutrient pollution in the Eastern Chinese coastal seas. WATER RESEARCH 2023; 231:119669. [PMID: 36716567 DOI: 10.1016/j.watres.2023.119669] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Harmful algal blooms (HABs) have been increasing in frequency, areal extent and duration due to the large increase in nutrient inputs from land-based sources to coastal seas, and cause significant economic losses. In this study, we used the "watershed-coast-continuum" concept to explore the effects of land-based nutrient pollution on HAB development in the Eastern Chinese coastal seas (ECCS). Results from the coupling of a watershed nutrient model and a coast hydrodynamic-biogeochemical model show that between the 1980s and 2000s, the risk of diatom blooms and dinoflagellate blooms increased by 158% and 127%, respectively. The spatial expansion of HAB risk caused by dinoflagellates is larger than that of diatoms. The simulated suitability of the habitat for bloom of Aureococcus anophagefferens, a pico-plankton of non-diatom or dinoflagellate, in the Bohai Sea is consistent with observations spatially and temporally. To halt further nutrient accumulation in the ECCS, reductions of dissolved inorganic nitrogen (DIN) (16%) and dissolved inorganic phosphorus (DIP) (33%) loading are required. To improve the situation of distorted DIN:DIP ratios, even larger reductions of DIN are required, especially in the Bohai Sea. Our approach is a feasible way to predict the risk of HABs under the pressure of increasing anthropogenic nutrient pollution in coastal waters.
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Affiliation(s)
- Hao Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Princetonlaan 8a, 3584 CB, Utrecht, the Netherlands; Research Center for Marine Ecology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Alexander F Bouwman
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Princetonlaan 8a, 3584 CB, Utrecht, the Netherlands; PBL Netherlands Environmental Assessment Agency, Postbus 30314, 2500 GH, The Hague, the Netherlands
| | | | | | - Arthur H W Beusen
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Princetonlaan 8a, 3584 CB, Utrecht, the Netherlands; PBL Netherlands Environmental Assessment Agency, Postbus 30314, 2500 GH, The Hague, the Netherlands
| | - Junjie Wang
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Princetonlaan 8a, 3584 CB, Utrecht, the Netherlands
| | - Xiaochen Liu
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Princetonlaan 8a, 3584 CB, Utrecht, the Netherlands
| | - Zhigang Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Xiangbin Ran
- Research Center for Marine Ecology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China.
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13
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Wetherbee R, Bringloe TT, van de Meene A, Andersen RA, Verbruggen H. Structure and formation of the perforated theca defining the Pelagophyceae (Heterokonta), and three new genera that substantiate the diverse nature of the class. JOURNAL OF PHYCOLOGY 2023; 59:126-151. [PMID: 36326615 DOI: 10.1111/jpy.13294] [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: 07/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The pelagophytes, a morphologically diverse class of marine heterokont algae, have been historically united only by DNA sequences. Recently we described a novel perforated theca (PT) encasing cells from the Pelagophyceae and hypothesized it may be the first morphological feature to define the class. Here we consolidate that observation, describing a PT for the first time in an additional seven pelagophyte genera, including three genera new to science. We established clonal cultures of pelagophytes collected from intertidal pools located around Australia, and established phylogenetic trees based on nuclear 18S rDNA and plastid rbcL, psaA, psaB, psbA and psbC gene sequences that led to the discovery of three new species: Wyeophycus julieharrissiae and Chromopallida australis form a distinct lineage along with Ankylochrysis lutea within the Pelagomonadales, while Pituiglomerulus capricornicus is sister genus to Chrysocystis fragilis in the Chrysocystaceae (Sarcinochrysidales). Using fixation by high-pressure freezing for electron microscope observations, a distinctive PT was observed in the three new genera described in this paper, as well as four genera not previously investigated: Chrysoreinhardia, Sargassococcus, Sungminbooa and Andersenia. The mechanism of PT formation is novel, being fabricated from rafts in Golgi-derived vesicles before being inserted into an established PT. Extracellular wall and/or mucilage layers assemble exterior to the PT in most pelagophytes, the materials likewise secreted by Golgi-derived vesicles, though the mechanism of secretion is novel. Secretory vesicles never fuse with the plasma membrane as in classic secretion and deposition, but rather relocate extracellularly beneath the PT and disintegrate, the contents having to pass through the PT prior to wall and/or mucilage synthesis. This study substantiates the diverse nature of pelagophytes, and provides further evidence that the PT is a sound morphological feature to define the Pelagophyceae, with all 14 of the 20 known genera studied to date by TEM possessing a PT.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Trevor T Bringloe
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Allison van de Meene
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, Washington, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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14
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Zhou Z, Kong F, Zhang Q, Gao Y, Koch F, Gobler CJ, Chen Z, Wang Y, Yu R. Brown tides linked to the unique nutrient profile in coastal waters of Qinhuangdao, China. ENVIRONMENTAL RESEARCH 2023; 216:114459. [PMID: 36181899 DOI: 10.1016/j.envres.2022.114459] [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: 08/13/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Brown tides caused by the pelagophyte Aureococcus anophagefferens have frequently occurred in the Bohai Sea since 2009 and have led to a dramatic collapse of the local scallop culture. To determine why brown tides occurred in the Bohai Sea rather than in other eutrophic coastal waters of China, phytoplankton communities and nutrients were evaluated and nutrient addition experiments were conducted in the Qinhuangdao coastal area. The concentration of dissolved organic nitrogen (DON) was nearly five times higher than that of dissolved inorganic nitrogen (DIN) during brown tides. High levels of phytoplankton biomass and nutrients were observed in the inshore waters, and the patterns of different nutrients were heterogeneous, which could be due to the uneven distribution of pelagophytes and non-brown tide phytoplankton populations (NBTP). The nutrient enrichment results indicated that the growth of the phytoplankton community was nitrogen-limited. Enrichment of DON, especially urea, could promote the growth of pelagophytes during the development stages of the brown tide. In brief, the results of this study imply that the unique nutrient profile (rich in DON but deficient in DIN) could support the outbreak of brown tides in the inshore waters of Qinhuangdao.
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Affiliation(s)
- Zhengxi Zhou
- 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, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China; Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fanzhou Kong
- 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, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China; Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Qingchun Zhang
- 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, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China; Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yan Gao
- China Ocean Mineral Resources R & D Association, Beijing, 100860, China
| | - Florian Koch
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 25570, Bremerhaven, Germany
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, 11968, USA; School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794-5000, USA
| | - Zhenfan Chen
- 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, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China
| | - Yunfeng Wang
- 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, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China; Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Rencheng Yu
- 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, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China; Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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15
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Pujari L, Kan J, Xin Y, Zhang G, Noman MA, Nilajkar S, Sun J. Deciphering the diversity and distribution of chromophytic phytoplankton in the Bohai Sea and the Yellow Sea via RuBisCO genes (rbcL). MARINE POLLUTION BULLETIN 2022; 184:114193. [PMID: 36209535 DOI: 10.1016/j.marpolbul.2022.114193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Present study investigated composition and distribution of chromophytic phytoplankton in the Bohai Sea (BS) and the Yellow Sea (YS) by using rbcL genes. Bacillariophyceae, Haptophyceae and Pelagophyceae were the most abundant phytoplankton groups. Distinct phytoplankton communities were observed in the BS and the YS: offshore stations were dominated by bloom forming genera Thalassiosira and Skeletonema, while brown tide-forming species including Chrysochromulina spp. and Aureococcus anophagefferens were commonly found in the nearshore areas. Redundancy analysis showed that phosphate, temperature and silicic acid play key roles in structuring chromophytic phytoplankton, such as phytoplankton at nearshore stations were affected by nutrient runoff from adjacent rivers (Yellow River). Anthropogenic activities in the Bohai Sea and seasonal circulation of ocean currents may also contribute to shaping chromophytic phytoplankton communities. This study provides data support and foundational observations of chromophytic phytoplankton in the BS and the YS, and their responses to environmental gradients and human activities.
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Affiliation(s)
- Laxman Pujari
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China; Business Development Group, National Institute of Oceanography, Goa, India; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, PA, USA
| | - Yehong Xin
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Guicheng Zhang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Md Abu Noman
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China
| | - Sujata Nilajkar
- Biological Oceanography Division, National Institute of Oceanography, Goa, India
| | - Jun Sun
- Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin 300457, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, China.
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16
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Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence. Commun Biol 2022; 5:983. [PMID: 36114260 PMCID: PMC9481584 DOI: 10.1038/s42003-022-03939-z] [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: 12/13/2021] [Accepted: 09/02/2022] [Indexed: 11/13/2022] Open
Abstract
The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata.
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17
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Selenoprotein: Potential Player in Redox Regulation in Chlamydomonas reinhardtii. Antioxidants (Basel) 2022; 11:antiox11081630. [PMID: 36009349 PMCID: PMC9404770 DOI: 10.3390/antiox11081630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/22/2022] Open
Abstract
Selenium (Se) is an essential micro-element for many organisms, including Chlamydomonas reinhardtii, and is required in trace amounts. It is obtained from the 21st amino acid selenocysteine (Sec, U), genetically encoded by the UGA codon. Proteins containing Sec are known as selenoproteins. In eukaryotes, selenoproteins are present in animals and algae, whereas fungi and higher plants lack them. The human genome contains 25 selenoproteins, most of which are involved in antioxidant defense activity, redox regulation, and redox signaling. In algae, 42 selenoprotein families were identified using various bioinformatics approaches, out of which C. reinhardtii is known to have 10 selenoprotein genes. However, the role of selenoproteins in Chlamydomonas is yet to be reported. Chlamydomonas selenoproteins contain conserved domains such as CVNVGC and GCUG, in the case of thioredoxin reductase, and CXXU in other selenoproteins. Interestingly, Sec amino acid residue is present in a catalytically active domain in Chlamydomonas selenoproteins, similar to human selenoproteins. Based on catalytical active sites and conserved domains present in Chlamydomonas selenoproteins, we suggest that Chlamydomonas selenoproteins could have a role in redox regulation and defense by acting as antioxidants in various physiological conditions.
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18
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Closed, Circular Genome Sequence of Aureococcus anophagefferens Virus, a Lytic Virus of a Brown Tide-Forming Alga. Microbiol Resour Announc 2022; 11:e0028222. [PMID: 35678577 PMCID: PMC9302175 DOI: 10.1128/mra.00282-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the genomic sequence of
Aureococcus anophagefferens
virus, assembled into one circular contig from both Nanopore and Illumina reads. The genome is 381,717 bp long with a GC content of 29.1%, which includes an additional 5-kb region between the previously predicted polar ends of the reference genome.
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19
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A Simple Model for a Fast Forewarning System of Brown Tide in the Coastal Waters of Qinhuangdao in the Bohai Sea, China. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12136477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Qinhuangdao, a famous coastal resort city in northeastern China, has been affected by the rapid growth of harmful algae. The brown tide induced by Aureococcus anophagefferens (A. anophagefferens) first occurred along Qinhuangdao’s coastline in 2009, and it then developed into a harmful alga for the Bohai Sea. Based on MIKE 21, we construct a 2D coupled hydrodynamic and transport model to study the variation and distribution of total nitrogen (TN), and establish the relationship between A. anophagefferens, dissolved organic nitrogen (DON), and TN to provide a fast forewarning system for brown tide in Qinhuangdao. This model considers the decay, diffusion, and settling of TN, and the model results are in good agreement with the measured tidal level, current, and TN, indicating that the model is capable of capturing the observed TN distribution during the brown tide period. The transfer function relating TN to A. anophagefferens leads to a reliable fast forewarning and monitoring system. Moreover, the transferred A. anophagefferens cell density can be used to forecast the regional risk level of brown tide with a specific color indicator. The implementation of national policy relating to marine ecosystems decreases the nearshore concentration of N, P, and other nutrients, and therefore decreases harmful algal blooms. The fast routine assessment of brown tide by the present warning system provides robust guidance for the government to take action.
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20
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Gilbertson R, Langan E, Mock T. Diatoms and Their Microbiomes in Complex and Changing Polar Oceans. Front Microbiol 2022; 13:786764. [PMID: 35401494 PMCID: PMC8991070 DOI: 10.3389/fmicb.2022.786764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/23/2022] [Indexed: 11/17/2022] Open
Abstract
Diatoms, a key group of polar marine microbes, support highly productive ocean ecosystems. Like all life on earth, diatoms do not live in isolation, and they are therefore under constant biotic and abiotic pressures which directly influence their evolution through natural selection. Despite their importance in polar ecosystems, polar diatoms are understudied compared to temperate species. The observed rapid change in the polar climate, especially warming, has created increased research interest to discover the underlying causes and potential consequences on single species to entire ecosystems. Next-Generation Sequencing (NGS) technologies have greatly expanded our knowledge by revealing the molecular underpinnings of physiological adaptations to polar environmental conditions. Their genomes, transcriptomes, and proteomes together with the first eukaryotic meta-omics data of surface ocean polar microbiomes reflect the environmental pressures through adaptive responses such as the expansion of protein families over time as a consequence of selection. Polar regions and their microbiomes are inherently connected to climate cycles and their feedback loops. An integrated understanding built on “omics” resources centered around diatoms as key primary producers will enable us to reveal unifying concepts of microbial co-evolution and adaptation in polar oceans. This knowledge, which aims to relate past environmental changes to specific adaptations, will be required to improve climate prediction models for polar ecosystems because it provides a unifying framework of how interacting and co-evolving biological communities might respond to future environmental change.
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Affiliation(s)
- Reuben Gilbertson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Emma Langan
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.,The Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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21
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Evolution of Phytoplankton as Estimated from Genetic Diversity. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10040456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phytoplankton are photosynthetic, single-celled organisms producing almost half of all oxygen on Earth and play a central role as prey for higher organisms, making them irreplaceable in the marine food web. As Global Change proceeds, imposing rapidly intensifying selection pressures, phytoplankton are forced to undergo evolution, local extinction, or redistribution, with potentially cascading effects throughout the marine ecosystem. Recent results from the field of population genetics display high levels of standing genetic diversity in natural phytoplankton populations, providing ample ‘evolutionary options’ and implying high adaptive potential to changing conditions. This potential for adaptive evolution is realized in several studies of experimental evolution, even though most of these studies investigate the evolution of only single strains. This, however, shows that phytoplankton not only evolve from standing genetic diversity, but also rely on de novo mutations. Recent global sampling campaigns show that the immense intraspecific diversity of phytoplankton in the marine ecosystem has been significantly underestimated, meaning we are only studying a minor portion of the relevant variability in the context of Global Change and evolution. An increased understanding of genomic diversity is primarily hampered by the low number of ecologically representative reference genomes of eukaryotic phytoplankton and the functional annotation of these. However, emerging technologies relying on metagenome and transcriptome data may offer a more realistic understanding of phytoplankton diversity.
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22
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Gann ER, Truchon AR, Papoulis SE, Dyhrman ST, Gobler CJ, Wilhelm SW. Aureococcus anophagefferens (Pelagophyceae) genomes improve evaluation of nutrient acquisition strategies involved in brown tide dynamics. JOURNAL OF PHYCOLOGY 2022; 58:146-160. [PMID: 34773248 DOI: 10.1111/jpy.13221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
The pelagophyte Aureococcus anophagefferens causes harmful brown tide blooms in marine embayments on three continents. Aureococcus anophagefferens was the first harmful algal bloom species to have its genome sequenced, an advance that evidenced genes important for adaptation to environmental conditions that prevail during brown tides. To expand the genomic tools available for this species, genomes for four strains were assembled, including three newly sequenced strains and one assembled from publicly available data. These genomes ranged from 57.11 to 73.62 Mb, encoding 13,191-17,404 potential proteins. All strains shared ~90% of their encoded proteins as determined by homology searches and shared most functional orthologs as determined by KEGG, although each strain also possessed coding sequences with unique functions. Like the original reference genome, the genomes assembled in this study possessed genes hypothesized to be important in bloom proliferation, including genes involved in organic compound metabolism and growth at low light. Cross-strain informatics and culture experiments suggest that the utilization of purines is a potentially important source of organic nitrogen for brown tides. Analyses of metatranscriptomes from a brown tide event demonstrated that use of a single genome yielded a lower read mapping percentage (~30% of library reads) as compared to a database generated from all available genomes (~43%), suggesting novel information about bloom ecology can be gained from expanding genomic space. This work demonstrates the continued need to sequence ecologically relevant algae to understand the genomic potential and their ecology in the environment.
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Affiliation(s)
- Eric R Gann
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Alexander R Truchon
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Spiridon E Papoulis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Sonya T Dyhrman
- Biology and Paleo Environment Division, Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York, 10964, USA
- Department of Earth and Environmental Sciences, Columbia University, Palisades, New York, 10964, USA
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11790, USA
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, 37996, USA
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23
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Lopez CB, Tilney CL, Muhlbach E, Bouchard JN, Villac MC, Henschen KL, Markley LR, Abbe SK, Shankar S, Shea C, Flewelling L, Garrett M, Badylak S, Phlips EJ, Hall LM, Lasi MA, Parks A, Paperno R, Adams DH, Edwards DD, Schneider JE, Wald KB, Biddle AR, Landers SL, Hubbard KA. High-resolution Spatiotemporal Dynamics of Harmful Algae in the Indian River Lagoon (Florida)-A Case Study of Aureoumbra lagunensis, Pyrodinium bahamense, and Pseudo- nitzschia. FRONTIERS IN MARINE SCIENCE 2021; 8:769877. [PMID: 37065006 PMCID: PMC10104561 DOI: 10.3389/fmars.2021.769877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The Indian River Lagoon (IRL), located on the east coast of Florida, is a complex estuarine ecosystem that is negatively affected by recurring harmful algal blooms (HABs) from distinct taxonomic/functional groups. Enhanced monitoring was established to facilitate rapid quantification of three recurrent bloom taxa, Aureoumbra lagunensis, Pyrodinium bahamense, and Pseudo-nitzschia spp., and included corroborating techniques to improve the identification of small-celled nanoplankton (<10 μm in diameter). Identification and enumeration of these target taxa were conducted during 2015-2020 using a combination of light microscopy and species-specific approaches, specifically immunofluorescence flow cytometry as well as a newly developed qPCR assay for A. lagunensis presented here for the first time. An annual bloom index (ABI) was established for each taxon based on occurrence and abundance data. Blooms of A. lagunensis (>2×108 cells L-1) were observed in all six years sampled and across multiple seasons. In contrast, abundance of P. bahamense, largely driven by the annual temperature cycle that moderates life cycle transitions and growth, displayed a strong seasonal pattern with blooms (105-107 cells L-1) generally developing in early summer and subsiding in autumn. However, P. bahamense bloom development was delayed and abundance was significantly lower in years and locations with sustained A. lagunensis blooms. Pseudo-nitzschia spp. were broadly distributed with sporadic bloom concentrations (reaching 107 cells L-1), but with minimal concentrations of the toxin domoic acid detected (<0.02 μg L-1). In summer 2020, multiple monitoring tools characterized a novel nano-cyanobacterium bloom (reaching 109 cells L-1) that coincided with a decline in A. lagunensis and persisted into autumn. Statistical and time-series analyses of this spatiotemporally intensive dataset highlight prominent patterns in variability for some taxa, but also identifies challenges of characterizing mechanisms underlying more episodic yet persistent events. Nevertheless, the intersect of temperature and salinity as environmental proxies proved to be informative in delineating niche partitioning, not only in the case of taxa with long-standing data sets but also for seemingly unprecedented blooms of novel nanoplanktonic taxa.
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Affiliation(s)
- Cary B Lopez
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Charles L Tilney
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Eric Muhlbach
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Josée N Bouchard
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Maria Célia Villac
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Karen L Henschen
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Laura R Markley
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Stephanie Keller Abbe
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Sugandha Shankar
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Colin Shea
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Leanne Flewelling
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Matthew Garrett
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
| | - Susan Badylak
- Fisheries and Aquatic Sciences Program, University of Florida, 7922 NW 71st Street, Gainesville, FL 32653, United States
| | - Edward J Phlips
- Fisheries and Aquatic Sciences Program, University of Florida, 7922 NW 71st Street, Gainesville, FL 32653, United States
| | - Lauren M Hall
- St. Johns River Water Management District (SJRWMD), 525 Community College Parkway, Palm Bay, FL 32909, United States
| | - Margaret A Lasi
- St. Johns River Water Management District (SJRWMD), PO Box 1429, Palatka, FL 32178, United States
| | - Ashley Parks
- St. Johns River Water Management District (SJRWMD), PO Box 1429, Palatka, FL 32178, United States
| | - Richard Paperno
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), Indian River Field Lab, 1220 Prospect Ave., # 285, Melbourne, FL 32901, United States
| | - Douglas H Adams
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), Indian River Field Lab, 1220 Prospect Ave., # 285, Melbourne, FL 32901, United States
| | - Dwayne D Edwards
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), Indian River Field Lab, 1220 Prospect Ave., # 285, Melbourne, FL 32901, United States
| | - Jacob E Schneider
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), Indian River Field Lab, 1220 Prospect Ave., # 285, Melbourne, FL 32901, United States
| | - Kyle B Wald
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), Indian River Field Lab, 1220 Prospect Ave., # 285, Melbourne, FL 32901, United States
| | - Autumn R Biddle
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), Indian River Field Lab, 1220 Prospect Ave., # 285, Melbourne, FL 32901, United States
| | - Shawna L Landers
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), Indian River Field Lab, 1220 Prospect Ave., # 285, Melbourne, FL 32901, United States
| | - Katherine A Hubbard
- Florida Fish and Wildlife Conservation Commission, Fish and Wildlife Research Institute (FWC-FWRI), 100 8 Ave. SE, St. Petersburg, FL 33701, United States
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24
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Liu Y, Hu Z, Deng Y, Shang L, Gobler CJ, Tang YZ. Dependence of genome size and copy number of rRNA gene on cell volume in dinoflagellates. HARMFUL ALGAE 2021; 109:102108. [PMID: 34815026 DOI: 10.1016/j.hal.2021.102108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Dinoflagellates are an ecologically important group of protists in aquatic environment and have evolved many unusual and enigmatic genomic features such as immense genome sizes, high repeated genes, and a large portion of hydroxymethyluracil in DNA. Although previous studies have observed positive correlations between the large subunit (LSU) rRNA gene copy number and genome size of a variety of eukaryotic organisms (e.g. higher plants and animals), or between cell volume and LSU rRNA gene copy number, and/or between genome size and cell size, which suggests a possible co-evolution among these three features in different lineages of life, it remains an open question regarding the relationships among these three parameters in dinoflagellates. For the first time, we estimated the copy numbers of the LSU rRNA gene, the genome sizes, and cell volumes within a broad range of dinoflagellates (covering 15 species of 11 genera) using single-cell qPCR-based assay (determining LSU rRNA gene copy number), FlowCAM (cell volume measurement), and ultraviolet spectrophotometry (genome size estimation). The measured copy number of LSU rRNA gene ranged from 398 ± 184 (Prorocentrum minimum) to 152,078 ± 33,555 copies•cell-1 (Alexandrium pacificum), while the genome size and the cell volume ranged from 5.6 ± 0.2 (Karlodinium veneficum) to 853 ± 19.9 pg•cell-1 (Pseliodinium pirum), and from 1,070 ± 225 (Kar. veneficum) to 168,474 ± 124,180 μm3 (Ps. pirum), respectively. Together with the three parameters measured in literature, there are significant positive linear correlations between LSU rRNA gene copy numbers and genome sizes, cell volumes and LSU rRNA gene copy numbers, and between genome sizes and cell volumes via comparisons of multi-model regression analyses, suggesting a dependence of genome size and rRNA gene copy number on the cell volumes of dinoflagellates. Validation of the measurement methods was conducted via comparisons between reported data in the literature and that predicted using the linear equations we obtained, and between genome size measured by flow cytometry (FCM) and ultraviolet spectrophotometry (Nanodrop). These results provide insightful understandings of dinoflagellate evolution in terms of the relationships among genomes, gene copy number, and cell volume, and of rRNA gene-based studies in intra-populational and intra-individual genetic diversity, taxonomy, and diversity assessment in the environment of dinoflagellates. The results also provide a dataset useful for reads calibration in environmental metabarcoding studies of dinoflagellates and selection of candidate species for whole genome sequencing.
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Affiliation(s)
- Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 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.
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 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
| | - Lixia Shang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 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
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11790, USA
| | - Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, 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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25
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Zhang QC, Yu RC, Zhao JY, Kong FZ, Chen ZF, Niu Z, Xiang L. Distribution of Aureococcus anophagefferens in relation to environmental factors and implications for brown tide seed sources in Qinhuangdao coastal waters, China. HARMFUL ALGAE 2021; 109:102105. [PMID: 34815018 DOI: 10.1016/j.hal.2021.102105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/01/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Brown tides caused by Aureococcus anophagefferens have occurred along the Qinhuangdao coastline in the Bohai Sea (BS) in recent years. Little is known about the spatio-temporal distribution of A. anophagefferens, particularly its profile distribution and the effects of environmental controls. In this study, four surveys were conducted in Qinhuangdao coastal waters during the brown tide from June to July 2013; another survey was conducted to cover a larger region in the BS in May 2016. Temperature, salinity, nutrients, and chlorophyll a were analyzed; and the density of A. anophagefferens was detected by a sensitive qPCR method. The intensive brown tide only occurred in Qinhuangdao inshore waters at temperatures ranging from 21.5 to 23.2 °C and relatively high salinity (> 29). Redundancy analysis indicated that the low dissolved inorganic nitrogen limited the growth of other pico- and nano-algal species; high dissolved organic nitrogen and low inorganic nutrients were suitable for the development of brown tides in Qinhuangdao coastal waters, which also contained a thermocline during the brown tide. At the early stage of the brown tide, a high abundance of A. anophagefferens appeared at the bottom of offshore waters characterized by low temperature and high salinity. The A. anophagefferens cells were speculated to originate from water mass located in a depression between the central ridge and the Qinhuangdao coastal area. In brief, this study reported the spatio-temporal variation of brown tides based on the abundance of A. anophagefferens and environmental forces and implied that A. anophagefferens could be transported from the bottom of offshore waters to promote brown tides in inshore waters of Qinhuangdao.
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Affiliation(s)
- Qing-Chun Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences,7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Ren-Cheng Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences,7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jia-Yu Zhao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences,7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan-Zhou Kong
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences,7 Nanhai Road, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhen-Fan Chen
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Zhuang Niu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences,7 Nanhai Road, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Xiang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences,7 Nanhai Road, Qingdao 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
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26
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Varasteh T, Tschoeke D, Silva-Lima AW, Thompson C, Thompson F. Transcriptome of the coral Mussismilia braziliensis symbiont Sargassococcus simulans. Mar Genomics 2021; 61:100912. [PMID: 34710723 DOI: 10.1016/j.margen.2021.100912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
A transcriptomic profile of Sargassococcus simulans 103B3, isolated from the coral Mussismilia braziliensis in Abrolhos, Brazil, is presented. A total of 631.3 Mbp transcriptomic sequences were obtained. The transcriptomic analysis disclosed transcripts coding for enzymes relevant for holobiont health including genes involved in I. Light harvesting complex (LHC), II. Organic matter utilization and III. Oxidative stress and microbial defense (Oxidoreductases) enzymes. The isolate exhibited transcripts for uptake and utilization of a variety of carbon sources, such as sugars, oligopeptides, and amino acids by ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) type transporters. Collectively, these enzymes indicate a mixotrophic metabolism in S. simulans with metabolic capabilities for the degradation of an array of organic carbon compounds in the coral Mussismilia and light harvesting within the low-light environments of Abrolhos.
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Affiliation(s)
- Tooba Varasteh
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Diogo Tschoeke
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Arthur W Silva-Lima
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Cristiane Thompson
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology and Sage-Coppe, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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27
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Sun S, Zhou J, Jiang J, Dai Y, Sheng M. Nitrile Hydratases: From Industrial Application to Acetamiprid and Thiacloprid Degradation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10440-10449. [PMID: 34469128 DOI: 10.1021/acs.jafc.1c03496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The widespread application of neonicotinoid insecticides (NEOs) in agriculture causes a series of environmental and ecological problems. Microbial remediation is a popular approach to relieve these negative impacts, but the associated molecular mechanisms are rarely explored. Nitrile hydratase (NHase), an enzyme commonly used in industry for amide production, was discovered to be responsible for the degradation of acetamiprid (ACE) and thiacloprid (THI) by microbes. Since then, research into NHases in NEO degradation has attracted increasing attention. In this review, microbial degradation of ACE and THI is briefly described. We then focus on NHase evolution, gene composition, maturation mechanisms, expression, and biochemical properties with regard to application of NHases in NEO degradation for bioremediation.
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Affiliation(s)
- Shilei Sun
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jiangsheng Zhou
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jihong Jiang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province and School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Yijun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Miaomiao Sheng
- College of Pharmacy, Zhejiang Chinese Medical University, Hangzhou 310053, People's Republic of China
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28
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Wang D, Zhang S, Zhang H, Lin S. Omics study of harmful algal blooms in China: Current status, challenges, and future perspectives. HARMFUL ALGAE 2021; 107:102079. [PMID: 34456014 DOI: 10.1016/j.hal.2021.102079] [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: 01/27/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
In the past two decades, the frequency, scale, and scope of harmful algal blooms (HABs) have increased significantly in the coastal waters of China. HABs have become a major ecological and environmental problem in China that seriously threatens the structure and function of marine ecosystems, the sustainable development of mariculture, and the health of human beings. Much effort has been devoted to studying HABs in China, and great achievements have been made in understanding the oceanographic and ecological mechanisms of HABs as well as the biology and physiological ecology of HAB-causing species. Furthermore, state-of-the-art omics technologies, such as transcriptomics and proteomics, have been used to elucidate the physiological responses of HAB-causing species to environmental changes, the biosynthesis of paralytic shellfish toxin, and the mechanisms underlying the formation of HABs. This review summarizes omics studies of HABs in China over the past few years and discusses challenges and future perspectives of HAB research.
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Affiliation(s)
- Dazhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Shufeng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Hao Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science/College of Ocean and Earth Science, Xiamen University, Xiamen 361102, China.
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29
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Wang W, Liao P, Li G, Chen H, Cen J, Lu S, Wong PK, An T. Photocatalytic inactivation and destruction of harmful microalgae Karenia mikimotoi under visible-light irradiation: Insights into physiological response and toxicity assessment. ENVIRONMENTAL RESEARCH 2021; 198:111295. [PMID: 33971128 DOI: 10.1016/j.envres.2021.111295] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/07/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Harmful algal blooms (HABs) caused by Karenia mikimotoi have frequently happened in coastal waters worldwide, causing serious damages to marine ecosystems and economic losses. Photocatalysis has potential to in-situ inhibit algal growth using sustainable sunlight. However, the inactivation and detoxification mechanisms of microalgae in marine environment have not been systematically investigated. In this work, for the first time, visible-light-driven photocatalytic inactivation of K. mikimotoi was attempted using g-C3N4/TiO2 immobilized films as a model photocatalyst. The inactivation efficiency could reach 64% within 60 min, evaluated by real-time in vivo chlorophyll-a fluorometric method. The immobilized photocatalyst films also exhibited excellent photo-stability and recyclability. Mechanisms study indicated photo-generated h+ and 1O2 were the dominant reactive species. Algal cell rupture process was monitored by fluorescent microscope combined with SEM observation, which confirmed the damage of cell membrane followed by the leakage of the intracellular components including the entire cell nucleus. The physiological responses regarding up-regulation of antioxidant enzyme activity (i.e. CAT and SOD), intracellular ROSs level and lipid peroxidation were all observed. Moreover, the intracellular release profile and acute toxicity assessment indicated the toxic K. mikimotoi was successfully detoxified, and the released organic matter had no cytotoxicity. This work not only provides a potential new strategy for in-situ treatment of K. mikimotoi using sunlight at sea environments, but also creates avenue for understanding the inactivation and destruction mechanisms of marine microalgae treated by photocatalysis and the toxicity impacts on the marine environments.
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Affiliation(s)
- Wanjun Wang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Pan Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Guiying Li
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Heng Chen
- Research Center of Harmful Algae and Marine Biology, Jinan University, Guangzhou, 510632, China
| | - Jingyi Cen
- Research Center of Harmful Algae and Marine Biology, Jinan University, Guangzhou, 510632, China
| | - Songhui Lu
- Research Center of Harmful Algae and Marine Biology, Jinan University, Guangzhou, 510632, China
| | - Po Keung Wong
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
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Gann ER, Kang Y, Dyhrman ST, Gobler CJ, Wilhelm SW. Metatranscriptome Library Preparation Influences Analyses of Viral Community Activity During a Brown Tide Bloom. Front Microbiol 2021; 12:664189. [PMID: 34135876 PMCID: PMC8200674 DOI: 10.3389/fmicb.2021.664189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
There is growing interest in the use of metatranscriptomics to study virus community dynamics. We used RNA samples collected from harmful brown tides caused by the eukaryotic alga Aureococcus anophagefferens within New York (United States) estuaries and in the process observed how preprocessing of libraries by either selection for polyadenylation or reduction in ribosomal RNA (rRNA) influenced virus community analyses. As expected, more reads mapped to the A. anophagefferens genome in polyadenylation-selected libraries compared to the rRNA-reduced libraries, with reads mapped in each sample correlating to one another regardless of preprocessing of libraries. Yet, this trend was not seen for reads mapping to the Aureococcus anophagefferens Virus (AaV), where significantly more reads (approximately two orders of magnitude) were mapped to the AaV genome in the rRNA-reduced libraries. In the rRNA-reduced libraries, there was a strong and significant correlation between reads mappings to AaV and A. anophagefferens. Overall, polyadenylation-selected libraries produced fewer viral contigs, fewer reads mapped to viral contigs, and different proportions across viral realms and families, compared to their rRNA-reduced pairs. This study provides evidence that libraries generated by rRNA reduction and not selected for polyadenylation are more appropriate for quantitative characterization of viral communities in aquatic ecosystems by metatranscriptomics.
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Affiliation(s)
- Eric R Gann
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Yoonja Kang
- Department of Ocean Integrated Science, School of Marine Technology, Chonnam National University, Yeosu, South Korea
| | - Sonya T Dyhrman
- Biology and Paleo Environment Division, Lamont-Doherty Earth Observatory, Columbia University, New York, NY, United States.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Steven W Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Knoxville, TN, United States
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31
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Naderi M, Puar P, Zonouzi-Marand M, Chivers DP, Niyogi S, Kwong RWM. A comprehensive review on the neuropathophysiology of selenium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:144329. [PMID: 33445002 DOI: 10.1016/j.scitotenv.2020.144329] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/05/2020] [Accepted: 12/05/2020] [Indexed: 05/25/2023]
Abstract
As an essential micronutrient, selenium (Se) exerts its biological function as a catalytic entity in a variety of enzymes. From a toxicological perspective, however, Se can become extremely toxic at concentrations slightly above its nutritional levels. Over the last few decades, there has been a growing level of concern worldwide regarding the adverse effects of both inorganic and organic Se compounds on a broad spectrum of neurological functions. A wealth of evidence has shown that exposure to excess Se may compromise the normal functioning of various key proteins, neurotransmitter systems (the glutamatergic, dopaminergic, serotonergic, and cholinergic systems), and signaling molecules involved in the control and regulation of cognitive, behavioral, and neuroendocrine functions. Elevated Se exposure has also been suspected to be a risk factor for the development of several neurodegenerative and neuropsychiatric diseases. Nonetheless, despite the various deleterious effects of excess Se on the central nervous system (CNS), Se neurotoxicity and negative behavioral outcomes are still disregarded at the expense of its beneficial health effects. This review focuses on the current state of knowledge regarding the neurobehavioral effects of Se and discusses its potential mode of action on different aspects of the central and peripheral nervous systems. This review also provides a brief history of Se discovery and uses, its physicochemical properties, biological roles in the CNS, environmental occurrence, and toxicity. We also review potential links between exposure to different forms of Se compounds and aberrant neurobehavioral functions in humans and animals, and identify key knowledge gaps and hypotheses for future research.
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Affiliation(s)
- Mohammad Naderi
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
| | - Pankaj Puar
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | | | - Douglas P Chivers
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
| | - Som Niyogi
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada; Toxicology Centre, University of Saskatchewan, 44 Campus Drive, Saskatoon, SK S7N 5B3, Canada
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32
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Wang S, Tang W, Delage E, Gifford S, Whitby H, González AG, Eveillard D, Planquette H, Cassar N. Investigating the microbial ecology of coastal hotspots of marine nitrogen fixation in the western North Atlantic. Sci Rep 2021; 11:5508. [PMID: 33750865 PMCID: PMC7943828 DOI: 10.1038/s41598-021-84969-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/27/2021] [Indexed: 11/24/2022] Open
Abstract
Variation in the microbial cycling of nutrients and carbon in the ocean is an emergent property of complex planktonic communities. While recent findings have considerably expanded our understanding of the diversity and distribution of nitrogen (N2) fixing marine diazotrophs, knowledge gaps remain regarding ecological interactions between diazotrophs and other community members. Using quantitative 16S and 18S V4 rDNA amplicon sequencing, we surveyed eukaryotic and prokaryotic microbial communities from samples collected in August 2016 and 2017 across the Western North Atlantic. Leveraging and significantly expanding an earlier published 2015 molecular dataset, we examined microbial community structure and ecological co-occurrence relationships associated with intense hotspots of N2 fixation previously reported at sites off the Southern New England Shelf and Mid-Atlantic Bight. Overall, we observed a negative relationship between eukaryotic diversity and both N2 fixation and net community production (NCP). Maximum N2 fixation rates occurred at sites with high abundances of mixotrophic stramenopiles, notably Chrysophyceae. Network analysis revealed such stramenopiles to be keystone taxa alongside the haptophyte diazotroph host Braarudosphaera bigelowii and chlorophytes. Our findings highlight an intriguing relationship between marine stramenopiles and high N2 fixation coastal sites.
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Affiliation(s)
- Seaver Wang
- Division of Earth and Ocean Sciences, Duke University, Grainger Environment Hall, 9 Circuit Drive, Box 90328, Durham, NC, 27708, USA
| | - Weiyi Tang
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Erwan Delage
- LS2N, UMR 6004, CNRS, Université de Nantes, 44000, Nantes, France
| | - Scott Gifford
- Department of Marine Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hannah Whitby
- Department of Earth, Ocean, and Ecological Sciences, School of Environmental Sciences, University of Liverpool, Liverpool, UK
| | - Aridane G González
- Instituto de Oceanografía y Cambio Global (IOCAG), Universidad de Las Palmas de Gran Canaria, ULPGC, Las Palmas, Spain.,Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroise, 13 Plouzané, 29280, Locmaria-Plouzané, France
| | - Damien Eveillard
- LS2N, UMR 6004, CNRS, Université de Nantes, 44000, Nantes, France
| | - Hélène Planquette
- Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroise, 13 Plouzané, 29280, Locmaria-Plouzané, France
| | - Nicolas Cassar
- Division of Earth and Ocean Sciences, Duke University, Grainger Environment Hall, 9 Circuit Drive, Box 90328, Durham, NC, 27708, USA. .,Laboratoire des Sciences de l'Environnement Marin (LEMAR), Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroise, 13 Plouzané, 29280, Locmaria-Plouzané, France.
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33
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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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34
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Sibbald SJ, Lawton M, Archibald JM. Mitochondrial Genome Evolution in Pelagophyte Algae. Genome Biol Evol 2021; 13:6126422. [PMID: 33675661 PMCID: PMC7936722 DOI: 10.1093/gbe/evab018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2021] [Indexed: 11/19/2022] Open
Abstract
The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756), and five strains of Aureoc. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984, and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 bp (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five Aureoc. anophagefferens strains varied slightly in length (42,401–42,621 bp) and were 99.4–100.0% identical. Gene content and order were highly conserved between the Aureoc. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in Aureoc. anophagefferens containingDNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. Although the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five Aureoc. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to nonbloom-forming species.
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Affiliation(s)
- Shannon J Sibbald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Maggie Lawton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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35
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Anderson DM, Fensin E, Gobler CJ, Hoeglund AE, Hubbard KA, Kulis DM, Landsberg JH, Lefebvre KA, Provoost P, Richlen ML, Smith JL, Solow AR, Trainer VL. Marine harmful algal blooms (HABs) in the United States: History, current status and future trends. HARMFUL ALGAE 2021; 102:101975. [PMID: 33875183 PMCID: PMC8058451 DOI: 10.1016/j.hal.2021.101975] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 05/04/2023]
Abstract
Harmful algal blooms (HABs) are diverse phenomena involving multiple. species and classes of algae that occupy a broad range of habitats from lakes to oceans and produce a multiplicity of toxins or bioactive compounds that impact many different resources. Here, a review of the status of this complex array of marine HAB problems in the U.S. is presented, providing historical information and trends as well as future perspectives. The study relies on thirty years (1990-2019) of data in HAEDAT - the IOC-ICES-PICES Harmful Algal Event database, but also includes many other reports. At a qualitative level, the U.S. national HAB problem is far more extensive than was the case decades ago, with more toxic species and toxins to monitor, as well as a larger range of impacted resources and areas affected. Quantitatively, no significant trend is seen for paralytic shellfish toxin (PST) events over the study interval, though there is clear evidence of the expansion of the problem into new regions and the emergence of a species that produces PSTs in Florida - Pyrodinium bahamense. Amnesic shellfish toxin (AST) events have significantly increased in the U.S., with an overall pattern of frequent outbreaks on the West Coast, emerging, recurring outbreaks on the East Coast, and sporadic incidents in the Gulf of Mexico. Despite the long historical record of neurotoxic shellfish toxin (NST) events, no significant trend is observed over the past 30 years. The recent emergence of diarrhetic shellfish toxins (DSTs) in the U.S. began along the Gulf Coast in 2008 and expanded to the West and East Coasts, though no significant trend through time is seen since then. Ciguatoxin (CTX) events caused by Gambierdiscus dinoflagellates have long impacted tropical and subtropical locations in the U.S., but due to a lack of monitoring programs as well as under-reporting of illnesses, data on these events are not available for time series analysis. Geographic expansion of Gambierdiscus into temperate and non-endemic areas (e.g., northern Gulf of Mexico) is apparent, and fostered by ocean warming. HAB-related marine wildlife morbidity and mortality events appear to be increasing, with statistically significant increasing trends observed in marine mammal poisonings caused by ASTs along the coast of California and NSTs in Florida. Since their first occurrence in 1985 in New York, brown tides resulting from high-density blooms of Aureococcus have spread south to Delaware, Maryland, and Virginia, while those caused by Aureoumbra have spread from the Gulf Coast to the east coast of Florida. Blooms of Margalefidinium polykrikoides occurred in four locations in the U.S. from 1921-2001 but have appeared in more than 15 U.S. estuaries since then, with ocean warming implicated as a causative factor. Numerous blooms of toxic cyanobacteria have been documented in all 50 U.S. states and the transport of cyanotoxins from freshwater systems into marine coastal waters is a recently identified and potentially significant threat to public and ecosystem health. Taken together, there is a significant increasing trend in all HAB events in HAEDAT over the 30-year study interval. Part of this observed HAB expansion simply reflects a better realization of the true or historic scale of the problem, long obscured by inadequate monitoring. Other contributing factors include the dispersion of species to new areas, the discovery of new HAB poisoning syndromes or impacts, and the stimulatory effects of human activities like nutrient pollution, aquaculture expansion, and ocean warming, among others. One result of this multifaceted expansion is that many regions of the U.S. now face a daunting diversity of species and toxins, representing a significant and growing challenge to resource managers and public health officials in terms of toxins, regions, and time intervals to monitor, and necessitating new approaches to monitoring and management. Mobilization of funding and resources for research, monitoring and management of HABs requires accurate information on the scale and nature of the national problem. HAEDAT and other databases can be of great value in this regard but efforts are needed to expand and sustain the collection of data regionally and nationally.
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Affiliation(s)
- Donald M Anderson
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States.
| | - Elizabeth Fensin
- NC Division of Water Resources, 4401 Reedy Creek Road, Raleigh, NC, 27607, United States
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, 11968, United States
| | - Alicia E Hoeglund
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, Florida, 33701, United States
| | - Katherine A Hubbard
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, Florida, 33701, United States
| | - David M Kulis
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States
| | - Jan H Landsberg
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, Florida, 33701, United States
| | - Kathi A Lefebvre
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, 98112, United States
| | - Pieter Provoost
- Intergovernmental Oceanographic Commission (IOC) of UNESCO, IOC Project Office for IODE, 8400 Oostende, Belgium
| | - Mindy L Richlen
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States
| | - Juliette L Smith
- Department of Aquatic Health Sciences, Virginia Institute of Marine Science, William & Mary, Gloucester Point, VA 23062, United States
| | - Andrew R Solow
- Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, United States
| | - Vera L Trainer
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA, 98112, United States
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36
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Paerl RW, Venezia RE, Sanchez JJ, Paerl HW. Picophytoplankton dynamics in a large temperate estuary and impacts of extreme storm events. Sci Rep 2020; 10:22026. [PMID: 33328574 PMCID: PMC7744581 DOI: 10.1038/s41598-020-79157-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/01/2020] [Indexed: 01/10/2023] Open
Abstract
Picophytoplankton (PicoP) are increasingly recognized as significant contributors to primary productivity and phytoplankton biomass in coastal and estuarine systems. Remarkably though, PicoP composition is unknown or not well-resolved in several large estuaries including the semi-lagoonal Neuse River Estuary (NRE), a tributary of the second largest estuary-system in the lower USA, the Pamlico-Albemarle Sound. The NRE is impacted by extreme weather events, including recent increases in precipitation and flooding associated with tropical cyclones. Here we examined the impacts of moderate to extreme (Hurricane Florence, September 2018) precipitation events on NRE PicoP abundances and composition using flow cytometry, over a 1.5 year period. Phycocyanin-rich Synechococcus-like cells were the most dominant PicoP, reaching ~ 106 cells mL-1, which highlights their importance as key primary producers in this relatively long residence-time estuary. Ephemeral "blooms" of picoeukaryotic phytoplankton (PEUK) during spring and after spikes in river flow were also detected, making PEUK periodically major contributors to PicoP biomass (up to ~ 80%). About half of the variation in PicoP abundance was explained by measured environmental variables. Temperature explained the most variation (24.5%). Change in total dissolved nitrogen concentration, an indication of increased river discharge, explained the second-most variation in PicoP abundance (15.9%). The short-term impacts of extreme river discharge from Hurricane Florence were particularly evident as PicoP biomass was reduced by ~ 100-fold for more than 2 weeks. We conclude that precipitation is a highly influential factor on estuarine PicoP biomass and composition, and show how 'wetter' future climate conditions will have ecosystem impacts down to the smallest of phytoplankton.
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Affiliation(s)
- Ryan W Paerl
- Department of Marine Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, 27695-8208, USA.
| | - Rebecca E Venezia
- Department of Marine Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, 27695-8208, USA
| | - Joel J Sanchez
- Department of Marine Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, 27695-8208, USA
| | - Hans W Paerl
- Institute of Marine Sciences, University of North Carolina At Chapel Hill, Morehead City, NC, 28557, USA
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Abstract
Background Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec but also the SECIS element in mRNA and the conservation of the Sec-flanking region. These unique features have led to the development of a series of bioinformatics methods to predict and research selenoprotein genes. There have been some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, has been very limited. Results In this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to record these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families. Conclusions This study reveals the primordial state of the eukaryotic selenoproteome. It is an important clue to explore the significance of selenium for primordial eukaryotes and to determine the complete evolutionary spectrum of selenoproteins in all life forms.
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Gann ER, Xian Y, Abraham PE, Hettich RL, Reynolds TB, Xiao C, Wilhelm SW. Structural and Proteomic Studies of the Aureococcus anophagefferens Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing. Front Microbiol 2020; 11:2047. [PMID: 33013751 PMCID: PMC7507832 DOI: 10.3389/fmicb.2020.02047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/04/2020] [Indexed: 01/28/2023] Open
Abstract
Viruses modulate the function(s) of environmentally relevant microbial populations, yet considerations of the metabolic capabilities of individual virus particles themselves are rare. We used shotgun proteomics to quantitatively identify 43 virus-encoded proteins packaged within purified Aureococcus anophagefferens Virus (AaV) particles, normalizing data to the per-virion level using a 9.5-Å-resolution molecular reconstruction of the 1900-Å (AaV) particle that we generated with cryogenic electron microscopy. This packaged proteome was used to determine similarities and differences between members of different giant virus families. We noted that proteins involved in sugar degradation and binding (e.g., carbohydrate lyases) were unique to AaV among characterized giant viruses. To determine the extent to which this virally encoded metabolic capability was ecologically relevant, we examined the TARA Oceans dataset and identified genes and transcripts of viral origin. Our analyses demonstrated that putative giant virus carbohydrate lyases represented up to 17% of the marine pool for this function. In total, our observations suggest that the AaV particle has potential prepackaged metabolic capabilities and that these may be found in other giant viruses that are widespread and abundant in global oceans.
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Affiliation(s)
- Eric R. Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Yuejiao Xian
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Paul E. Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Todd B. Reynolds
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuan Xiao
- Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Zhao YX, Yang WL, Guo L, Jiang HY, Cheng X, Dai YJ. Bioinformatics of a Novel Nitrile Hydratase Gene Cluster of the N 2-Fixing Bacterium Microvirga flocculans CGMCC 1.16731 and Characterization of the Enzyme. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:9299-9307. [PMID: 32786837 DOI: 10.1021/acs.jafc.0c03702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microvirga flocculans CGMCC 1.16731 can degrade many cyano group-containing neonicotinoid insecticides. Here, its genome was sequenced, and a novel nitrile hydratase gene cluster was discovered in a plasmid. The NHase gene cluster (pnhF) has gene structure β-subunit 1, α-subunit, and β-subunit 2, which is different from previously reported NHase gene structures. Phylogenetic analysis of α-subunits indicated that NHases containing the three subunit (β1αβ2) structure are independent from NHases containing two subunits (αβ). pnhF was successfully expressed in Escherichia coli, and the purified PnhF could convert the nitrile-containing insecticide flonicamid to N-(4-trifluoromethylnicotinoyl)glycinamide. The enzymatic properties of PnhF were investigated using flonicamid as a substrate. Homology models revealed that amino acid residue β1-Glu56 may strongly affect the catalytic activity of PnhF. This study expands our understanding of the structures and functions of NHases and the enzymatic mechanism of the environmental fate of flonicamid.
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Affiliation(s)
- Yun-Xiu Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Wen-Long Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Ling Guo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Huo-Yong Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Xi Cheng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
| | - Yi-Jun Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Science, Nanjing Normal University, Nanjing 210023, People's Republic of China
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Santesmasses D, Mariotti M, Gladyshev VN. Bioinformatics of Selenoproteins. Antioxid Redox Signal 2020; 33:525-536. [PMID: 32031018 PMCID: PMC7409585 DOI: 10.1089/ars.2020.8044] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 12/13/2022]
Abstract
Significance: Bioinformatics has brought important insights into the field of selenium research. The progress made in the development of computational tools in the last two decades, coordinated with growing genome resources, provided new opportunities to study selenoproteins. The present review discusses existing tools for selenoprotein gene finding and other bioinformatic approaches to study the biology of selenium. Recent Advances: The availability of complete selenoproteomes allowed assessing a global distribution of the use of selenocysteine (Sec) across the tree of life, as well as studying the evolution of selenoproteins and their biosynthetic pathway. Beyond gene identification and characterization, human genetic variants in selenoprotein genes were used to examine adaptations to selenium levels in diverse human populations and to estimate selective constraints against gene loss. Critical Issues: The synthesis of selenoproteins is essential for development in mice. In humans, several mutations in selenoprotein genes have been linked to rare congenital disorders. And yet, the mechanism of Sec insertion and the regulation of selenoprotein synthesis in mammalian cells are not completely understood. Future Directions: Omics technologies offer new possibilities to study selenoproteins and mechanisms of Sec incorporation in cells, tissues, and organisms.
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Affiliation(s)
- Didac Santesmasses
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Marco Mariotti
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
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41
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Zhang Y, Zheng J. Bioinformatics of Metalloproteins and Metalloproteomes. Molecules 2020; 25:molecules25153366. [PMID: 32722260 PMCID: PMC7435645 DOI: 10.3390/molecules25153366] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Correspondence: ; Tel.: +86-755-2692-2024
| | - Junge Zheng
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
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Liu C, Shi X, Wu F, Ren M, Gao G, Wu Q. Genome analyses provide insights into the evolution and adaptation of the eukaryotic Picophytoplankton Mychonastes homosphaera. BMC Genomics 2020; 21:477. [PMID: 32652928 PMCID: PMC7354681 DOI: 10.1186/s12864-020-06891-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/07/2020] [Indexed: 12/31/2022] Open
Abstract
Background Picophytoplankton are abundant and can contribute greatly to primary production in eutrophic lakes. Mychonastes species are among the common eukaryotic picophytoplankton in eutrophic lakes. We used third-generation sequencing technology to sequence the whole genome of Mychonastes homosphaera isolated from Lake Chaohu, a eutrophic freshwater lake in China. Result The 24.23 Mbp nuclear genome of M.homosphaera, harboring 6649 protein-coding genes, is more compact than the genomes of the closely related Sphaeropleales species. This genome streamlining may be caused by a reduction in gene family number, intergenic size and introns. The genome sequence of M.homosphaera reveals the strategies adopted by this organism for environmental adaptation in the eutrophic lake. Analysis of cultures and the protein complement highlight the metabolic flexibility of M.homosphaera, the genome of which encodes genes involved in light harvesting, carbohydrate metabolism, and nitrogen and microelement metabolism, many of which form functional gene clusters. Reconstruction of the bioenergetic metabolic pathways of M.homosphaera, such as the lipid, starch and isoprenoid pathways, reveals characteristics that make this species suitable for biofuel production. Conclusion The analysis of the whole genome of M. homosphaera provides insights into the genome streamlining, the high lipid yield, the environmental adaptation and phytoplankton evolution.
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Affiliation(s)
- Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Fan Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingdong Ren
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal. Sci Rep 2020; 10:9449. [PMID: 32523048 PMCID: PMC7287063 DOI: 10.1038/s41598-020-65941-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.
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Cheng Z, Xia Y, Zhou Z. Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications. Front Bioeng Biotechnol 2020; 8:352. [PMID: 32391348 PMCID: PMC7193024 DOI: 10.3389/fbioe.2020.00352] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.
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Affiliation(s)
| | | | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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45
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Gann ER, Hughes BJ, Reynolds TB, Wilhelm SW. Internal Nitrogen Pools Shape the Infection of Aureococcus anophagefferens CCMP 1984 by a Giant Virus. Front Microbiol 2020; 11:492. [PMID: 32269558 PMCID: PMC7109300 DOI: 10.3389/fmicb.2020.00492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/06/2020] [Indexed: 11/13/2022] Open
Abstract
The pelagophyte Aureococcus anophagefferens blooms annually in shallow bays around the world, where it is hypothesized to outcompete other phytoplankton in part by using alternative nitrogen sources. The high proportion of natural populations that are infected during the late stages of the bloom suggest viruses cause bloom collapse. We hypothesized that the Aureococcus anophagefferens Virus (AaV) infection cycle would be negatively influenced in cultures acclimated to decreasing external nitrogen conditions, but that the real-time external nitrogen concentration would not influence the infection cycle. Cultures acclimated in NO 3 - concentrations (0.0147 mM; N:P = 0.1225) that showed reduced end point cell abundances, forward scatter (a proxy for size) and red fluorescence (a proxy for chlorophyll a), also produced fewer viruses per cell at a slower rate. Decreasing the external concentration of nitrogen post infection did not alter burst size or time to lysis. These data suggest that the nitrogen used for new viral progeny is present within host cells at the time of infection. Flow cytometric data of an infection cycle showed a reduction in red fluorescence around twelve hours post infection, consistent with degradation of nitrogen-rich chloroplasts during the infection cycle. Using cell and virus quota estimates, we determined that A. anophagefferens cells had sufficient nitrogen and carbon for the lower ranges of burst sizes determined but did not contain enough phosphorous. Consistent with this observation, expression of nitrate and sugar transporters did not increase in the publicly available transcriptome data of the infection cycle, while several phosphorus transporters were. Our data demonstrate that dynamics of viruses infecting Aureococcus over the course of a bloom is dictated by the host cell state upon infection, which is set a priori by external nutrient supplies.
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Affiliation(s)
- Eric R Gann
- Department of Microbiology, College of Arts and Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Brennan J Hughes
- Department of Microbiology, College of Arts and Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Todd B Reynolds
- Department of Microbiology, College of Arts and Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Steven W Wilhelm
- Department of Microbiology, College of Arts and Sciences, The University of Tennessee, Knoxville, Knoxville, TN, United States
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Liu S, Gibson K, Cui Z, Chen Y, Sun X, Chen N. Metabarcoding analysis of harmful algal species in Jiaozhou Bay. HARMFUL ALGAE 2020; 92:101772. [PMID: 32113606 DOI: 10.1016/j.hal.2020.101772] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/23/2020] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
Accurate detection of the composition and dynamics of harmful algal bloom (HAB) species is critical for studying the mechanisms of HAB formation and for developing means for predicting the occurrences of HABs. Jiaozhou Bay is an epitome of China's coastal ecosystem and an ideal site for HAB research with the accumulation of decades of historical investigation records. Nevertheless, most of these earlier studies on phytoplankton communities applied primarily morphology-based approaches with limited resolution in phytoplankton species identification, especially for those with small-sized cells and for cryptic species. Through analyzing samples collected at 12 spatially isolated locations using metabarcoding methods, 89 phytoplankton species, including 34 Bacillariophyta, 25 Dinoflagellata, 7 Cryptophyta, 11 Chlorophyta, 8 Ochrophyta and 2 Haptophyta species were detected. Of those, 70 species had never been reported in Jiaozhou Bay in the previous expedition investigations, demonstrating the strength of the metabarcoding analysis approach. The distribution of many algal species demonstrated unique patterns, which were likely influenced by interactions among phytoplankton species or by predation by groups such as Ciliophora and Cercozoa, in addition to environmental factors such as temperature and nutritional conditions. Among these algal species, 28 were annotated as HAB species, among which 13 were reported for the very first time in Jiaozhou Bay including a mixtotrophic dianoflagellate Heterocapsa rotundata and a chain-forming diatom Skeletonema marinoi, both ranked among the top 10 most abundant ASVs. The present study represents a first attempt to study HAB species and other phytoplankton species in Jiaozhou Bay using the metabarcoding approach, which revealed substantially more algal species in Jiaozhou Bay than previously identified and sets a solid foundation for further research on the mechanisms of HAB formation.
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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; 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
| | - Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - 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; University of Chinese Academy of Sciences, Beijing, 100049, 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; University of Chinese Academy of Sciences, Beijing, 100049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaoxia Sun
- 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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Gann ER, Gainer PJ, Reynolds TB, Wilhelm SW. Influence of light on the infection of Aureococcus anophagefferens CCMP 1984 by a "giant virus". PLoS One 2020; 15:e0226758. [PMID: 31899921 PMCID: PMC6941929 DOI: 10.1371/journal.pone.0226758] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/03/2019] [Indexed: 11/18/2022] Open
Abstract
The pelagophyte Aureococcus anophagefferens has caused recurrent brown tide blooms along the northeast coast of the United States since the mid-1980's, and more recently spread to other regions of the globe. These blooms, due to the high cell densities, are associated with severe light attenuation that destroys the sea grass beds which provide the basis for many fisheries. Data collected by transmission electron microscopy, PCR, and metatranscriptomic studies of the blooms, support the hypothesis that large dsDNA viruses play a role in bloom dynamics. While a large (~140 nm) icosahedral virus, with a 371 kbp genome, was first isolated more than a decade ago, the constraints imposed by environmental parameters on bloom infection dynamics by Aureococcus anophagefferens Virus, (AaV) remain unknown. To investigate the role light plays in infection by this virus, we acclimated A. anophagefferens to light intensities of 30 (low), 60 (medium) or 90 μmol photons m-2 s-1 (high) and infected cultures at these irradiance levels. Moreover, we completed light shift experiments where acclimated cultures were exposed to even lower light intensities (0, 5, and 15 μmol photons m-2 s-1) consistent with irradiance found during the peak of the bloom when cell concentrations are highest. The abundance of viruses produced per lytic event (burst size) was lower in the low irradiance acclimated cultures compared to the medium and high acclimated cultures. Transferring infected cultures to more-limiting light availabilities further decreased burst size and increased the length of time it took for cultures to lyse, regardless of acclimation irradiance level. A hypothetical mechanism for the reduced efficiency of the infection cycle in low light due to ribosome biogenesis was predicted from pre-existing transcriptomes. Overall, these studies provide a framework for understanding light effects on infection dynamics over the course of the summer months when A. anophagefferens blooms occur.
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Affiliation(s)
- Eric R. Gann
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - P. Jackson Gainer
- Department of Biology, Tennessee Wesleyan University, Athens, Tennessee, United States of America
| | - Todd B. Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Steven W. Wilhelm
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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Hennon GMM, Dyhrman ST. Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms. HARMFUL ALGAE 2020; 91:101587. [PMID: 32057337 DOI: 10.1016/j.hal.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/10/2023]
Abstract
Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.
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Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.
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Raven JA, Gobler CJ, Hansen PJ. Dynamic CO 2 and pH levels in coastal, estuarine, and inland waters: Theoretical and observed effects on harmful algal blooms. HARMFUL ALGAE 2020; 91:101594. [PMID: 32057340 DOI: 10.1016/j.hal.2019.03.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 06/10/2023]
Abstract
Rising concentrations of atmospheric CO2 results in higher equilibrium concentrations of dissolved CO2 in natural waters, with corresponding increases in hydrogen ion and bicarbonate concentrations and decreases in hydroxyl ion and carbonate concentrations. Superimposed on these climate change effects is the dynamic nature of carbon cycling in coastal zones, which can lead to seasonal and diel changes in pH and CO2 concentrations that can exceed changes expected for open ocean ecosystems by the end of the century. Among harmful algae, i.e. some species and/or strains of Cyanobacteria, Dinophyceae, Prymnesiophyceae, Bacillariophyceae, and Ulvophyceae, the occurrence of a CO2 concentrating mechanisms (CCMs) is the most frequent mechanism of inorganic carbon acquisition in natural waters in equilibrium with the present atmosphere (400 μmol CO2 mol-1 total gas), with varying phenotypic modification of the CCM. No data on CCMs are available for Raphidophyceae or the brown tide Pelagophyceae. Several HAB species and/or strains respond to increased CO2 concentrations with increases in growth rate and/or cellular toxin content, however, others are unaffected. Beyond the effects of altered C concentrations and speciation on HABs, changes in pH in natural waters are likely to have profound effects on algal physiology. This review outlines the implications of changes in inorganic cycling for HABs in coastal zones, and reviews the knowns and unknowns with regard to how HABs can be expected to ocean acidification. We further point to the large regions of uncertainty with regard to this evolving field.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK; Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia; School of Biological Science, University of Western Australia, Crawley, WA, 6009, Australia.
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton NY, 11968, USA.
| | - Per Juel Hansen
- University of Copenhagen, Marine Biological Section, Strandpromenaden 5, DK 3000 Helsingør, Denmark
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50
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Abstract
Selenium is an essential trace element for maintenance of overall health, whose deficiency and dyshomeostasis have been linked to a variety of diseases and disorders. The majority of previous researches focused on characterization of genes encoding selenoproteins or proteins involved in selenium metabolism as well as their functions. Many studies in humans also investigated the relationship between selenium and complex diseases, but their results have been inconsistent. In recent years, systems biology and "-omics" approaches have been widely used to study complex and global variations of selenium metabolism and function in physiological and different pathological conditions. The present paper reviews recent progress in large-scale and systematic analyses of the relationship between selenium status or selenoproteins and several complex diseases, mainly including population-based cohort studies and meta-analyses, genetic association studies, and some other omics-based studies. Advances in ionomics and its application in studying the interaction between selenium and other trace elements in human health and diseases are also discussed.
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Affiliation(s)
- Huimin Ying
- Department of Endocrinology, Xixi Hospital of Hangzhou, Hangzhou, 310023, Zhejiang, People's Republic of China
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, Guangdong, People's Republic of China.
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