1
|
Jian J, Wu Z, Silva-Núñez A, Li X, Zheng X, Luo B, Liu Y, Fang X, Workman CT, Larsen TO, Hansen PJ, Sonnenschein EC. Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168042. [PMID: 37898203 DOI: 10.1016/j.scitotenv.2023.168042] [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: 08/21/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKS) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Overlap with repeats and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.
Collapse
Affiliation(s)
- Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Arisbe Silva-Núñez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Tecnologico de Monterrey, School of Engineering and Science, Monterrey, Nuevo León, Mexico
| | - Xiaohui Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Bei Luo
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yun Liu
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Per Juel Hansen
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Department of Biosciences, Swansea University, Swansea, United Kingdom.
| |
Collapse
|
2
|
Hehenberger E, Guo J, Wilken S, Hoadley K, Sudek L, Poirier C, Dannebaum R, Susko E, Worden AZ. Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias. Mol Biol Evol 2023; 40:msad251. [PMID: 37987557 PMCID: PMC10735309 DOI: 10.1093/molbev/msad251] [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: 04/17/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023] Open
Abstract
Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in "light stress." The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.
Collapse
Affiliation(s)
- Elisabeth Hehenberger
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, CZ
| | - Jian Guo
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Susanne Wilken
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kenneth Hoadley
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
| | - Lisa Sudek
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Camille Poirier
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
| | - Richard Dannebaum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, CA
| | - Alexandra Z Worden
- Ocean EcoSystems Biology Unit, RD3, GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, DE
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- Max Planck Institute for Evolutionary Biology, 24306 Plön, DE
| |
Collapse
|
3
|
Song Y, Li R, Song W, Tang Y, Sun S, Mao G. Microcystis spp. and phosphorus in aquatic environments: A comprehensive review on their physiological and ecological interactions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163136. [PMID: 37001662 DOI: 10.1016/j.scitotenv.2023.163136] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/02/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023]
Abstract
Cyanobacterial blooms caused by eutrophication have become a major environmental problem in aquatic ecosystems worldwide over the last few decades. Phosphorus is a limiting nutrient that affects the growth of cyanobacteria and plays a role in dynamic changes in algal density and the formation of cyanobacterial blooms. Therefore, identifying the association between phosphorus sources and Microcystis, which is the most representative and harmful cyanobacteria, is essential for building an understanding of the ecological risks of cyanobacterial blooms. However, systematic reviews summarizing the relationships between Microcystis and phosphorus in aquatic environments are rare. Thus, this study provides a comprehensive overview of the physiological and ecological interactions between phosphorus sources and Microcystis in aquatic environments from the following perspectives: (i) the effects of phosphorus source and concentration on Microcystis growth, (ii) the impacts of phosphorus on the environmental behaviors of Microcystis, (iii) mechanisms of phosphorus-related metabolism in Microcystis, and (iv) role of Microcystis in the distribution of phosphorus sources within aquatic environments. In addition, relevant unsolved issues and essential future investigations (e.g., secondary ecological risks) have been highlighted and discussed. This review provides deeper insights into the relationship between phosphorus sources and Microcystis and can serve as a reference for the evaluation, monitoring, and effective control of cyanobacterial blooms.
Collapse
Affiliation(s)
- Yuhao Song
- School of Life Sciences, Qufu Normal University, Qufu 273165, China.
| | - Ruikai Li
- School of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Wenjia Song
- School of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Yulu Tang
- School of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Shuangyan Sun
- School of Life Sciences, Qufu Normal University, Qufu 273165, China
| | - Guannan Mao
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
4
|
Sobieraj J, Metelski D. Insights into Toxic Prymnesium parvum Blooms as a Cause of the Ecological Disaster on the Odra River. Toxins (Basel) 2023; 15:403. [PMID: 37368703 PMCID: PMC10302719 DOI: 10.3390/toxins15060403] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
In 2022, Poland and Germany experienced a prolonged and extensive mass fish kill in the Odra River. During the period from the end of July to the beginning of September 2022, a high level of incidental disease and mortality was observed in various fish species (dozens of different species were found dead). The fish mortality affected five Polish provinces (Silesia, Opole, Lower Silesia, Lubuskie, and Western Pomerania) and involved reservoir systems covering most of the river (the Odra River is 854 km long, of which 742 km are in Poland). Fatal cases were investigated using toxicological, anatomopathological, and histopathological tests. Water samples were collected to determine nutrient status in the water column, phytoplankton biomass, and community composition. High nutrient concentrations indicated high phytoplankton productivity, with favorable conditions for golden algal blooms. The harmful toxins (prymnesins secreted by Prymnesium parvum habitats) had not been found in Poland before, but it was only a matter of time, especially in the Odra River, whose waters are permanently saline and still used for navigation. The observed fish mortality resulted in a 50% decrease in the fish population in the river and affected mainly cold-blooded species. Histopathological examinations of fish showed acute damage to the most perfused organs (gills, spleen, kidneys). The disruption to hematopoietic processes and damage to the gills were due to the action of hemolytic toxins (prymnesins). An evaluation of the collected hydrological, meteorological, biological, and physico-chemical data on the observed spatio-temporal course of the catastrophe, as well as the detection of three compounds from the group of B-type prymnesins in the analyzed material (the presence of prymnesins was confirmed using an analysis of the fragmentation spectrum and the accurate tandem mass spectrometry (MS/MS) measurement, in combination with high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS), allowed the formulation and subsequent testing of the hypothesis for a direct link between the observed fish mortality and the presence of prymnesins in the Odra River. This article systematizes what is known about the causes of the fish kill in the Odra River in 2022, based on official government reports (one Polish and one German) and the EU technical report by the Joint Research Centre. A review and critical analysis of government findings (Polish and German) on this disaster were conducted in the context of what is known to date about similar cases of mass fish kills.
Collapse
Affiliation(s)
- Janusz Sobieraj
- Department of Building Engineering, Warsaw University of Technology, 00-637 Warsaw, Poland;
| | - Dominik Metelski
- Research Group SEJ-609 “AMIKO”, Faculty of Economics and Management Sciences, Campus de Cartuja s/n, University of Granada, 18071 Granada, Spain
| |
Collapse
|
5
|
Caron DA, Lie AAY, Buckowski T, Turner J, Frabotta K. The Effect of pH and Salinity on the Toxicity and Growth of the Golden Alga, Prymnesium parvum. Protist 2023; 174:125927. [PMID: 36565615 DOI: 10.1016/j.protis.2022.125927] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Bioassays using cultures of the toxic haptophyte Prymnesium parvum and the ciliate Cyclidium sp. as prey were conducted to test the effect of pH (range = 6.5 - 8.5), salinity (range = 1.50 - 7.50‰), and a combination of pH and salinity on the toxicity of P. parvum. pH had a significant effect on P. parvum toxicity. Toxicity was rapidly (within 24 hr) induced by increasing pH of the medium, or reduced by lowering pH. Conversely, lowering salinity reduced toxicity, albeit less effectively compared to pH, and P. parvum cells remained toxic at the lowest values tested (1.50‰ at pH 7.5). An additional effect between pH and salinity was also observed: low salinity combined with low pH led to not only decreased toxicity, but also resulted in lower P. parvum growth rates. Such effects of pH and salinity on P. parvum growth and toxicity provide insight into the environmental factors supporting community dominance and toxic blooms of the alga.
Collapse
Affiliation(s)
- David A Caron
- Aquatic EcoTechnologies, LLC, Santa Cruz, CA 95065, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Alle A Y Lie
- Aquatic EcoTechnologies, LLC, Santa Cruz, CA 95065, USA
| | - Tom Buckowski
- Lake Mission Viejo Association, Mission Viejo, CA 92692, USA
| | - Jim Turner
- Lake Mission Viejo Association, Mission Viejo, CA 92692, USA
| | - Kevin Frabotta
- Lake Mission Viejo Association, Mission Viejo, CA 92692, USA
| |
Collapse
|
6
|
Koppelle S, López-Escardó D, Brussaard CPD, Huisman J, Philippart CJM, Massana R, Wilken S. Mixotrophy in the bloom-forming genus Phaeocystis and other haptophytes. HARMFUL ALGAE 2022; 117:102292. [PMID: 35944956 DOI: 10.1016/j.hal.2022.102292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 05/13/2023]
Abstract
Phaeocystis is a globally widespread marine phytoplankton genus, best known for its colony-forming species that can form large blooms and odorous foam during bloom decline. In the North Sea, Phaeocystis globosa typically becomes abundant towards the end of the spring bloom, when nutrients are depleted and the share of mixotrophic protists increases. Although mixotrophy is widespread across the eukaryotic tree of life and is also found amongst haptophytes, a mixotrophic nutrition has not yet been demonstrated in Phaeocystis. Here, we sampled two consecutive Phaeocystis globosa spring blooms in the coastal North Sea. In both years, bacterial cells were observed inside 0.6 - 2% of P. globosa cells using double CARD-FISH hybridizations in combination with laser scanning confocal microscopy. Incubation experiments manipulating light and nutrient availability showed a trend towards higher occurrence of intracellular bacteria under P-deplete conditions. Based on counts of bacteria inside P. globosa cells in combination with theoretical values of prey digestion times, maximum ingestion rates of up to 0.08 bacteria cell-1 h-1 were estimated. In addition, a gene-based predictive model was applied to the transcriptome assemblies of seven Phaeocystis strains and 24 other haptophytes to assess their trophic mode. This model predicted a phago-mixotrophic feeding strategy in several (but not all) strains of P. globosa, P. antarctica and other haptophytes that were previously assumed to be autotrophic. The observation of bacterial cells inside P. globosa and the gene-based model predictions strongly suggest that the phago-mixotrophic feeding strategy is widespread among members of the Phaeocystis genus and other haptophytes, and might contribute to their remarkable success to form nuisance blooms under nutrient-limiting conditions.
Collapse
Affiliation(s)
- Sebastiaan Koppelle
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands.
| | - David López-Escardó
- Ecology of Marine Microbes, Institut de Ciènces del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Corina P D Brussaard
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands; Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Jef Huisman
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands
| | - Catharina J M Philippart
- Department of Coastal Systems, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands; Department of Physical Geography, Utrecht University, P.O. Box 80115, 3508 TC, Utrecht, The Netherlands
| | - Ramon Massana
- Ecology of Marine Microbes, Institut de Ciènces del Mar (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain
| | - Susanne Wilken
- Department of Freshwater and Marine Ecology (FAME), Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94920, 1090 XH, Amsterdam, The Netherlands.
| |
Collapse
|
7
|
Ji N, Wang J, Zhang Z, Chen L, Xu M, Yin X, Shen X. Transcriptomic response of the harmful algae Heterosigma akashiwo to polyphosphate utilization and phosphate stress. HARMFUL ALGAE 2022; 117:102267. [PMID: 35944950 DOI: 10.1016/j.hal.2022.102267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/24/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Phosphorus (P) is one of the major macronutrients necessary for phytoplankton growth. In some parts of the ocean, however, P is frequently scarce, hence, there is limited phytoplankton growth. To cope with P deficiency, phytoplankton evolved a variety of strategies, including, utilization of different P sources. Polyphosphate (polyP) is ubiquitously present and serves an essential function in aquatic environments, but it is unclear if and how this polymer is utilized by phytoplankton. Here, we examined the physiological and molecular responses of the widely present harmful algal bloom (HAB) species, Heterosigma akashiwo in polyP utilization, and in coping with P-deficiency. Our results revealed that two forms of inorganic polyP, namely, sodium tripolyphosphate and sodium hexametaphosphate, support H. akashiwo growth as efficiently as orthophosphate. However, few genes involved in polyP utilization have been identified. Under P-deficient conditions, genes associated with P transport, dissolved organic P utilization, sulfolipid synthesis, and energy production, were markedly elevated. In summary, our results indicate that polyP is bioavailable to H. akashiwo, and this HAB species have evolved a comprehensive strategy to cope with P deficiency.
Collapse
Affiliation(s)
- Nanjing Ji
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Marine Resources Development Research Institute, Lianyungang 222005, China; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Junyue Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhenzhen Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Lei Chen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Mingyang Xu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xueyao Yin
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xin Shen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China.
| |
Collapse
|
8
|
Efficient treatment of phenol wastewater by co-culture of Chlorella vulgaris and Candida tropicalis. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
|
9
|
Shi JQ, Ou-Yang T, Yang SQ, Zhao L, Ji LL, Wu ZX. Transcriptomic responses to phosphorus in an invasive cyanobacterium, Raphidiopsis raciborskii: Implications for nutrient management. HARMFUL ALGAE 2022; 111:102150. [PMID: 35016763 DOI: 10.1016/j.hal.2021.102150] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/26/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Phosphorus (P) is a vital macronutrient associated with the growth and proliferation of Raphidiopsis raciborskii, an invasive and notorious bloom-forming cyanobacterium. However, the molecular mechanisms involved in P acclimation remain largely unexplored for Raphidiopsis raciborskii. Here, transcriptome sequencing of Raphidiopsis raciborskii was conducted to reveal multifaceted mechanisms involved in mimicking dipotassium phosphate (DIP), β-glycerol phosphate (Gly), 2-aminoethylphosphonic acid (AEP), and P-free conditions (NP). Chlorophyll a fluorescence parameters showed significant differences in the NP and AEP groups compared with the DIP and Gly-groups. Expression levels of genes related to phosphate transportation and uptake, organic P utilization, nitrogen metabolism, urea cycling, carbon fixation, amino acid metabolism, environmental information, the ATP-synthesis process in glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway were remarkably upregulated, while those related to photosynthesis, phycobiliproteins, respiration, oxidative phosphorylation, sulfur metabolism, and genetic information were markedly downregulated in the NP group relative to the DIP group. However, the expression of genes involved in organic P utilization, the urea cycle, and genetic information in the Gly-group, and carbon-phosphorus lyase, genetic information and environmental information in the AEP group were significantly increased compared to the DIP group. Together, these results indicate that Raphidiopsis raciborskii exhibits the evolution of coordination of multiple metabolic pathways and certain key genes to adapt to ambient P changes, which implies that if P is reduced to control Raphidiopsis raciborskii bloom, there is a risk that external nutrients (such as nitrogen, amino acids, and urea) will stimulate the growth or metabolism of Raphidiopsis.
Collapse
Affiliation(s)
- Jun-Qiong Shi
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, P. R. China
| | - Tian Ou-Yang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, P. R. China
| | - Song-Qi Yang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, P. R. China
| | - Lu Zhao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, P. R. China
| | - Lu-Lu Ji
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, P. R. China
| | - Zhong-Xing Wu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Science, Southwest University, Chongqing 400715, P. R. China.
| |
Collapse
|
10
|
Yu Q, He J, Zhao Q, Wang X, Zhi Y, Li X, Li X, Li L, Ge B. Regulation of nitrogen source for enhanced photobiological H2 production by co-culture of Chlamydomonas reinhardtii and Mesorhizobium sangaii. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
11
|
Soós V, Shetty P, Maróti G, Incze N, Badics E, Bálint P, Ördög V, Balázs E. Biomolecule composition and draft genome of a novel, high-lipid producing Scenedesmaceae microalga. ALGAL RES 2021. [DOI: 10.1016/j.algal.2020.102181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
12
|
Jimenez V, Burns JA, Le Gall F, Not F, Vaulot D. No evidence of Phago-mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic. JOURNAL OF PHYCOLOGY 2021; 57:435-446. [PMID: 33394518 DOI: 10.1111/jpy.13125] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/28/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phago-mixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.
Collapse
Affiliation(s)
- Valeria Jimenez
- Ecology of Marine Plankton, Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - John A Burns
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Florence Le Gall
- Ecology of Marine Plankton, Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Fabrice Not
- Ecology of Marine Plankton, Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Daniel Vaulot
- Ecology of Marine Plankton, Sorbonne Université, CNRS, UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
- Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| |
Collapse
|
13
|
Kawai S, Martinez JN, Lichtenberg M, Trampe E, Kühl M, Tank M, Haruta S, Nishihara A, Hanada S, Thiel V. In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat. Microorganisms 2021; 9:microorganisms9030652. [PMID: 33801086 PMCID: PMC8004040 DOI: 10.3390/microorganisms9030652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO2 fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O2 and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L−1 O2). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions.
Collapse
Affiliation(s)
- Shigeru Kawai
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
- Correspondence: (S.K.); (V.T.)
| | - Joval N. Martinez
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Department of Natural Sciences, College of Arts and Sciences, University of St. La Salle, Bacolod City, Negros Occidental 6100, Philippines
| | - Mads Lichtenberg
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Erik Trampe
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Michael Kühl
- Department of Biology, Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (M.L.); (E.T.); (M.K.)
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8566, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan; (J.N.M.); (M.T.); (S.H.); (A.N.); (S.H.)
- DSMZ—German Culture Collection of Microorganisms and Cell Culture, GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
- Correspondence: (S.K.); (V.T.)
| |
Collapse
|
14
|
Shi X, Xiao Y, Liu L, Xie Y, Ma R, Chen J. Transcriptome responses of the dinoflagellate Karenia mikimotoi driven by nitrogen deficiency. HARMFUL ALGAE 2021; 103:101977. [PMID: 33980427 DOI: 10.1016/j.hal.2021.101977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
The availability of ambient N nutrient is often correlated with the occurrences of harmful algal bloom formed by certain dinoflagellates, making it important to understand how these species might be responding to such conditions. Here, transcriptome sequencing of Karenia mikimotoi was conducted to understand the underlying molecular mechanisms by which this dinoflagellate copes with nitrogen (N) deficiency. Transcriptomic analysis revealed 8802 unigenes (3.56%) that were differentially expressed with ≥ 2-fold change. Under N-depleted conditions, genes involved in glycolysis, fatty acid metabolism, and the tricarboxylic acid (TCA) cycle as well as lipid accumulation were significantly upregulated. The elevated expression of enzymes used in protein degradation and turnover suggests possible metabolic reconfiguration towards accelerated N recycling. Moreover, a significant increase in urea transporter was observed, indicating increased assimilation of organic nitrogen resources as an alternative in N-depleted cultures of K. mikimotoi. The down-regulated glutamate synthase genes were also identified under N deficiency, suggesting suppression of primary amino acid synthesis to save N resource. Taken together, results of this study show enhanced multiple N resource acquisition and reuse of multiple N resources constitute a comprehensive strategy to cope with N deficiency in a dinoflagellate.
Collapse
Affiliation(s)
- Xinguo Shi
- Fujian Engineering Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fujian 350116, China; Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China.
| | - Yuchun Xiao
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China
| | - Lemian Liu
- Fujian Engineering Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fujian 350116, China; Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China
| | - Youping Xie
- Fujian Engineering Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fujian 350116, China; Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China
| | - Ruijuan Ma
- Fujian Engineering Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fujian 350116, China; Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China
| | - Jianfeng Chen
- Fujian Engineering Research Center for Comprehensive Utilization of Marine Products Waste, Fuzhou University, Fujian 350116, China; Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fujian 350116, China.
| |
Collapse
|
15
|
Beedessee G, Kubota T, Arimoto A, Nishitsuji K, Waller RF, Hisata K, Yamasaki S, Satoh N, Kobayashi J, Shoguchi E. Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate. BMC Biol 2020; 18:139. [PMID: 33050904 PMCID: PMC7557087 DOI: 10.1186/s12915-020-00873-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Our understanding of dinoflagellate toxin biosynthesis has been hampered by their unusually large genomes. To overcome this challenge, for the first time, we sequenced the genome, microRNAs, and mRNA isoforms of a basal dinoflagellate, Amphidinium gibbosum, and employed an integrated omics approach to understand its secondary metabolite biosynthesis. RESULTS We assembled the ~ 6.4-Gb A. gibbosum genome, and by probing decoded dinoflagellate genomes and transcriptomes, we identified the non-ribosomal peptide synthetase adenylation domain as essential for generation of specialized metabolites. Upon starving the cells of phosphate and nitrogen, we observed pronounced shifts in metabolite biosynthesis, suggestive of post-transcriptional regulation by microRNAs. Using Iso-Seq and RNA-seq data, we found that alternative splicing and polycistronic expression generate different transcripts for secondary metabolism. CONCLUSIONS Our genomic findings suggest intricate integration of various metabolic enzymes that function iteratively to synthesize metabolites, providing mechanistic insights into how dinoflagellates synthesize secondary metabolites, depending upon nutrient availability. This study provides insights into toxin production associated with dinoflagellate blooms. The genome of this basal dinoflagellate provides important clues about dinoflagellate evolution and overcomes the large genome size, which has been a challenge previously.
Collapse
Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
- Present address: Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
| | - Takaaki Kubota
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Onomichi, Hiroshima, 722-0073, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Shinichi Yamasaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Jun'ichi Kobayashi
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| |
Collapse
|
16
|
Ji N, Zhang Z, Huang J, Zhou L, Deng S, Shen X, Lin S. Utilization of various forms of nitrogen and expression regulation of transporters in the harmful alga Heterosigma akashiwo (Raphidophyceae). HARMFUL ALGAE 2020; 92:101770. [PMID: 32113589 DOI: 10.1016/j.hal.2020.101770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 01/01/2020] [Accepted: 01/31/2020] [Indexed: 06/10/2023]
Abstract
Nitrogen (N) is an essential nutrient for phytoplankton growth. There is ample evidence that N enrichment promotes harmful algae blooms (HABs) but molecular mechanisms regulating N-nutrient uptake and metabolism are not so clear, especially for the raphidophyte Heterosigma akashiwo, which forms ichthyotoxic HABs in many coastal waters. In this study, the utilization of three different chemical forms of N (nitrate, ammonium, and urea) by H. akashiwo CCMA 369 was investigated in batch culture conditions. Results showed that H. akashiwo grew well on all three N compounds, and the highest cell yield occurred in the NH4+ culture group. Reverse transcription quantitative PCR analysis revealed that the expression of high-affinity NO3- transporter (NIT), NH4+ transporter (AMT) and high-affinity urea active transporter (DUR3), were significantly up-regulated under N-limitation compared to the N-replete control. The mRNA levels of AMT and DUR3 also displayed a clear diel rhythm, with high levels at midnight. In addition, NH4+ addition (5 μM) did not depress the transcript abundance of any of the three N transporters. Compared with the co-occurring immobile diatom Skeletonema costatum, the high expression of AMT in dark period in H. akashiwo is consistent with its diel vertical migration behavior, which may promote N-nutrient acquisition from deeper layers and give advantages for H. akashiwo to form blooms.
Collapse
Affiliation(s)
- Nanjing Ji
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, 361005, China; Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA
| | - Zhenzhen Zhang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Jinwang Huang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Lingjie Zhou
- Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA
| | - Shengxian Deng
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Xin Shen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, 222005, China; Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, 361005, China; Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA.
| |
Collapse
|
17
|
Transcriptional and physiological responses to inorganic nutrition in a tropical Pacific strain of Alexandrium minutum: Implications for nutrient uptakes and assimilation. Gene 2019; 711:143950. [PMID: 31255736 DOI: 10.1016/j.gene.2019.143950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 11/22/2022]
Abstract
The marine dinoflagellate Alexandrium minutum is known to produce saxitoxins that cause paralytic shellfish poisoning in human worldwide through consumption of the contaminated shellfish mollusks. Despite numerous studies on the growth physiology and saxitoxin production of this species, the knowledge on the molecular basis of nutrient uptakes in relation to toxin production in this species is limited. In this study, relative expressions of the high-affinity transporter genes of nitrate, ammonium, and phosphate (AmNrt2, AmAmt1 and AmPiPT1) and the assimilation genes, nitrate reductase (AmNas), glutamine synthase (AmGSIII) and carbamoyl phosphate synthase (AmCPSII) from A. minutum were studied in batch clonal culture condition with two nitrogen sources (nitrate: NO3- or ammonium: NH4+) under different N:P ratios (high-P: N:P of 14 and 16, and low-P: N:P of 155). The expression of AmAmt1 was suppressed in excess NH4+-grown condition but was not observed in AmNrt2 and AmNas. Expressions of AmAmt1, AmNrt2, AmNas, AmGSIII, AmCPSII, and AmPiPT1 were high in P-deficient condition, showing that A. minutum is likely to take up nutrients for growth under P-stress condition. Conversely, relative expression of AmCPSII was incongruent with cell growth, but was well correlated with toxin quota, suggesting that the gene might involve in arginine metabolism and related toxin production pathway. The expression of AmGSIII is found coincided with higher toxin production and is believed to involve in mechanism to detoxify the cells from excess ammonium stress. The gene regulation observed in this study has provided better insights into the ecophysiology of A. minutum in relation to its adaptive strategies in unfavorable environments.
Collapse
|
18
|
Cáceres C, Spatharis S, Kaiserli E, Smeti E, Flowers H, Bonachela JA. Temporal phosphate gradients reveal diverse acclimation responses in phytoplankton phosphate uptake. ISME JOURNAL 2019; 13:2834-2845. [PMID: 31350454 DOI: 10.1038/s41396-019-0473-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 06/11/2019] [Accepted: 06/28/2019] [Indexed: 11/10/2022]
Abstract
Phytoplankton face environmental nutrient variations that occur in the dynamic upper layers of the ocean. Phytoplankton cells are able to rapidly acclimate to nutrient fluctuations by adjusting their nutrient-uptake system and metabolism. Disentangling these acclimation responses is a critical step in bridging the gap between phytoplankton cellular physiology and community ecology. Here, we analyzed the dynamics of phosphate (P) uptake acclimation responses along different P temporal gradients by using batch cultures of the diatom Phaeodactylum tricornutum. We employed a multidisciplinary approach that combined nutrient-uptake bioassays, transcriptomic analysis, and mathematical models. Our results indicated that cells increase their maximum nutrient-uptake rate (Vmax) both in response to P pulses and strong phosphorus limitation. The upregulation of three genes coding for different P transporters in cells experiencing low intracellular phosphorus levels supported some of the observed Vmax variations. In addition, our mathematical model reproduced the empirical Vmax patterns by including two types of P transporters upregulated at medium-high environmental and low intracellular phosphorus levels, respectively. Our results highlight the existence of a sequence of acclimation stages along the phosphate continuum that can be understood as a succession of acclimation responses. We provide a novel conceptual framework that can contribute to integrating and understanding the dynamics and wide diversity of acclimation responses developed by phytoplankton.
Collapse
Affiliation(s)
- Carlos Cáceres
- Department of Mathematics and Statistics, University of Strathclyde, Livingstone Tower, 26 Richmond St., Glasgow, Scotland, G1 1XH, UK. .,Schiermeier Olentangy River Wetland Research Park, School of Environment and Natural Resources, The Ohio State University, Columbus, OH, 43202, USA.
| | - Sofie Spatharis
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.,School of Life Sciences, University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Evangelia Smeti
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Ave., Anavyssos, 19013, Greece
| | - Hugh Flowers
- Department of Chemistry, University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
| | - Juan A Bonachela
- Department of Mathematics and Statistics, University of Strathclyde, Livingstone Tower, 26 Richmond St., Glasgow, Scotland, G1 1XH, UK. .,Department of Ecology, Evolution, and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ, 08901, USA.
| |
Collapse
|
19
|
Deodato CR, Barlow SB, Hovde BT, Cattolico RA. Naked Chrysochromulina (Haptophyta) isolates from lake and river ecosystems: An electron microscopic comparison including new observations on the type species of this taxon. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
20
|
Zuo Z, Yang Y, Xu Q, Yang W, Zhao J, Zhou L. Effects of phosphorus sources on volatile organic compound emissions from Microcystis flos-aquae and their toxic effects on Chlamydomonas reinhardtii. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2018; 40:1283-1298. [PMID: 29264818 DOI: 10.1007/s10653-017-0055-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
There is diverse phosphorus (P) in eutrophicated waters, but it is considered as a crucial nutrient for cyanobacteria growth due to its easy precipitation as insoluble salts. To uncover the effects of complex P nutrients on the emission of volatile organic compounds (VOCs) from cyanobacteria and their toxic effects on other algae, the VOCs from Microcystis flos-aquae supplied with different types and amount of P nutrients were analyzed, and the effects of VOCs and their two main compounds on Chlamydomonas reinhardtii growth were investigated. When M. flos-aquae cells were supplied with K2HPO4, sodium pyrophosphate and sodium hexametaphosphate as the sole P source, 27, 23 and 29 compounds were found, respectively, including furans, sulfocompounds, terpenoids, benzenes, aldehydes, hydrocarbons and esters. With K2HPO4 as the sole P source, the VOC emission increased with reducing P amount, and the maximum emission was found under Non-P condition. In the treatments of M. flos-aquae VOCs under Non-P condition and two main terpenoids (eucalyptol and limonene) in the VOCs, remarkable decreases were found in C. reinhardtii cell growth, photosynthetic pigment content and photosynthetic abilities. Therefore, we deduce that multiple P nutrients in eutrophicated waters induce different VOC emissions from cyanobacteria, and P amount reduction caused by natural precipitation and algal massive growth results in more VOC emissions. These VOCs play toxic roles in cyanobacteria becoming dominant species, and eucalyptol and limonene are two toxic agents.
Collapse
Affiliation(s)
- Zhaojiang Zuo
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China.
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
| | - Youyou Yang
- College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Qinghuan Xu
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Wangting Yang
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Jingxian Zhao
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Lv Zhou
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| |
Collapse
|
21
|
Hu SK, Liu Z, Alexander H, Campbell V, Connell PE, Dyhrman ST, Heidelberg KB, Caron DA. Shifting metabolic priorities among key protistan taxa within and below the euphotic zone. Environ Microbiol 2018; 20:2865-2879. [PMID: 29708635 DOI: 10.1111/1462-2920.14259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/12/2022]
Abstract
A metatranscriptome study targeting the protistan community was conducted off the coast of Southern California, at the San Pedro Ocean Time-series station at the surface, 150 m (oxycline), and 890 m to link putative metabolic patterns to distinct protistan lineages. Comparison of relative transcript abundances revealed depth-related shifts in the nutritional modes of key taxonomic groups. Eukaryotic gene expression in the sunlit surface environment was dominated by phototrophs, such as diatoms and chlorophytes, and high abundances of transcripts associated with synthesis pathways (e.g., photosynthesis, carbon fixation, fatty acid synthesis). Sub-euphotic depths (150 and 890 m) exhibited strong contributions from dinoflagellates and ciliates, and were characterized by transcripts relating to digestion or intracellular nutrient recycling (e.g., breakdown of fatty acids and V-type ATPases). These transcriptional patterns underlie the distinct nutritional modes of ecologically important protistan lineages that drive marine food webs, and provide a framework to investigate trophic dynamics across diverse protistan communities.
Collapse
Affiliation(s)
- Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Harriet Alexander
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, USA
| | - Victoria Campbell
- Division Allergy and Infectious Diseases, UW Medicine, Seattle, WA, USA
| | - Paige E Connell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA
| | - Karla B Heidelberg
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
22
|
Gong W, Paerl H, Marchetti A. Eukaryotic phytoplankton community spatiotemporal dynamics as identified through gene expression within a eutrophic estuary. Environ Microbiol 2018; 20:1095-1111. [PMID: 29349913 DOI: 10.1111/1462-2920.14049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/18/2017] [Accepted: 01/12/2018] [Indexed: 01/13/2023]
Abstract
Over the span of a year, we investigated the interactions between biotic and abiotic factors within the eutrophic Neuse River Estuary (NRE). Through metatranscriptomic sequencing in combination with water quality measurements, we show that there are different metabolic strategies deployed along the NRE. In the upper estuary, taxonomically resolved phytoplankton groups express more transcripts of genes for synthesis of cellular components and carbon metabolism whereas in the lower estuary, transcripts allocated to nutrient metabolism and transport were more highly expressed. Metabolisms for polysaccharide synthesis and transportation were elevated in the lower estuary and could be reflective of unbalanced growth and/or interactions with their surrounding microbial consortia. Our results indicate phytoplankton have high metabolic activity, suggestive of increased growth rates in the upper estuary and display patterns reflective of nutrient limitation in the lower estuary. Among all the environmental parameters varying along the NRE, nitrogen availability is found to be the main driving factor for the observed spatial divergence.
Collapse
Affiliation(s)
- Weida Gong
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Murray Hall, 123 South Rd, Chapel Hill, NC 27514, USA
| | - Hans Paerl
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, 3431 Arendell Street, Morehead City, NC 28557, USA
| | - Adrian Marchetti
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Murray Hall, 123 South Rd, Chapel Hill, NC 27514, USA
| |
Collapse
|
23
|
Ji N, Lin L, Li L, Yu L, Zhang Y, Luo H, Li M, Shi X, Wang DZ, Lin S. Metatranscriptome analysis reveals environmental and diel regulation of a Heterosigma akashiwo
(raphidophyceae) bloom. Environ Microbiol 2018; 20:1078-1094. [DOI: 10.1111/1462-2920.14045] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 01/09/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Nanjing Ji
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
- Department of Marine Sciences; University of Connecticut; Groton CT 06340 USA
| | - Lingxiao Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Meizhen Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Xinguo Shi
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences; Xiamen University; Xiamen Fujian 361102 China
- Department of Marine Sciences; University of Connecticut; Groton CT 06340 USA
| |
Collapse
|
24
|
Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2018. [DOI: 10.3390/jmse6010013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
25
|
RNA-Seq as an Emerging Tool for Marine Dinoflagellate Transcriptome Analysis: Process and Challenges. Processes (Basel) 2018. [DOI: 10.3390/pr6010005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
26
|
Jing X, Lin S, Zhang H, Koerting C, Yu Z. Utilization of urea and expression profiles of related genes in the dinoflagellate Prorocentrum donghaiense. PLoS One 2017; 12:e0187837. [PMID: 29117255 PMCID: PMC5678928 DOI: 10.1371/journal.pone.0187837] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/26/2017] [Indexed: 01/23/2023] Open
Abstract
Urea has been shown to contribute more than half of total nitrogen (N) required by phytoplankton in some estuaries and coastal waters and to provide a substantial portion of the N demand for many harmful algal blooms (HABs) of dinoflagellates. In this study, we investigated the physiological and transcriptional responses in Prorocentrum donghaiense to changes in nitrate and urea availability. We found that this species could efficiently utilize urea as sole N source and achieve comparable growth rate and photosynthesis capability as it did under nitrate. These physiological parameters were markedly lower in cultures grown under nitrate- or urea-limited conditions. P. donghaiense N content was similarly low under nitrate- or urea-limited culture condition, but was markedly higher under urea-replete condition than under nitrate-replete condition. Carbon (C) content was consistently elevated under N-limited condition. Consequently, the C:N ratio was as high as 21:1 under nitrate- or urea-limitation, but 7:1 under urea-replete condition and 9:1 to 10:1 under nitrate-replete condition. Using quantitative reverse transcription PCR, we investigated the expression pattern for four genes involved in N transport and assimilation. The results indicated that genes encoding nitrate transport, urea hydrolysis, and nickel transporter gene were sensitive to changes in general N nutrient availability whereas the urea transporter gene responded much more strongly to changes in urea concentration. Taken together, our study shows the high bioavailability of urea, its impact on C:N stoichiometry, and the sensitivity of urea transporter gene expression to urea availability.
Collapse
Affiliation(s)
- Xiaoli Jing
- College of Marine Life Science, Ocean University of China, Qingdao, China
- Department of Marine Sciences, University of Connecticut, Groton, United States of America
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, United States of America
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, United States of America
| | - Claudia Koerting
- Department of Marine Sciences, University of Connecticut, Groton, United States of America
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao, China
| |
Collapse
|
27
|
Haley ST, Alexander H, Juhl AR, Dyhrman ST. Transcriptional response of the harmful raphidophyte Heterosigma akashiwo to nitrate and phosphate stress. HARMFUL ALGAE 2017; 68:258-270. [PMID: 28962986 DOI: 10.1016/j.hal.2017.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 06/30/2017] [Accepted: 07/01/2017] [Indexed: 06/07/2023]
Abstract
The marine eukaryotic alga Heterosigma akashiwo (Raphidophyceae) is known for forming ichthyotoxic harmful algal blooms (HABs). In the past 50 years, H. akashiwo blooms have increased, occurring globally in highly eutrophic coastal and estuarine systems. These systems often incur dramatic physicochemical changes, including macronutrient (nitrogen and phosphorus) enrichment and depletion, on short timescales. Here, H. akashiwo cultures grown under nutrient replete, low N and low P growth conditions were examined for changes in biochemical and physiological characteristics in concert with transcriptome sequencing to provide a mechanistic perspective on the metabolic processes involved in responding to N and P stress. There was a marked difference in the overall transcriptional pattern between low N and low P transcriptomes. Both nutrient stresses led to significant changes in the abundance of thousands of contigs related to a wide diversity of metabolic pathways, with limited overlap between the transcriptomic responses to low N and low P. Enriched contigs under low N included many related to nitrogen metabolism, acquisition, and transport. In addition, metabolic modules like photosynthesis and carbohydrate metabolism changed significantly under low N, coincident with treatment-specific changes in photosynthetic efficiency and particulate carbohydrate content. P-specific contigs responsible for P transport and organic P use were more enriched in the low P treatment than in the replete control and low N treatment. These results provide new insight into the genetic mechanisms that distinguish how this HAB species responds to these two common nutrient stresses, and the results can inform future field studies, linking transcriptional patterns to the physiological ecology of H. akashiwo in situ.
Collapse
Affiliation(s)
- Sheean T Haley
- Columbia University, Lamont-Doherty Earth Observatory, Palisades, NY, USA
| | - Harriet Alexander
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Andrew R Juhl
- Columbia University, Lamont-Doherty Earth Observatory, Palisades, NY, USA; Columbia University, Department of Earth and Environmental Sciences, Palisades, NY, USA
| | - Sonya T Dyhrman
- Columbia University, Lamont-Doherty Earth Observatory, Palisades, NY, USA; Columbia University, Department of Earth and Environmental Sciences, Palisades, NY, USA.
| |
Collapse
|
28
|
Harke MJ, Juhl AR, Haley ST, Alexander H, Dyhrman ST. Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae. Front Microbiol 2017; 8:1279. [PMID: 28769884 PMCID: PMC5513979 DOI: 10.3389/fmicb.2017.01279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/26/2017] [Indexed: 11/13/2022] Open
Abstract
The concentration and composition of bioavailable nitrogen (N) and phosphorus (P) in the upper ocean shape eukaryotic phytoplankton communities and influence their physiological responses. Phytoplankton are known to exhibit similar physiological responses to limiting N and P conditions such as decreased growth rates, chlorosis, and increased assimilation of N and P. Are these responses similar at the molecular level across multiple species? To interrogate this question, five species from biogeochemically important, bloom-forming taxa (Bacillariophyta, Dinophyta, and Haptophyta) were grown under similar low N, low P, and replete nutrient conditions to identify transcriptional patterns and associated changes in biochemical pools related to N and P stress. Metabolic profiles, revealed through the transcriptomes of these taxa, clustered together based on species rather than nutrient stressor, suggesting that the global metabolic response to nutrient stresses was largely, but not exclusively, species-specific. Nutrient stress led to few transcriptional changes in the two dinoflagellates, consistent with other research. An orthologous group analysis examined functionally conserved (i.e., similarly changed) responses to nutrient stress and therefore focused on the diatom and haptophytes. Most conserved ortholog changes were specific to a single nutrient treatment, but a small number of orthologs were similarly changed under both N and P stress in 2 or more species. Many of these orthologs were related to photosynthesis and may represent generalized stress responses. A greater number of orthologs were conserved across more than one species under low P compared to low N. Screening the conserved orthologs for functions related to N and P metabolism revealed increased relative abundance of orthologs for nitrate, nitrite, ammonium, and amino acid transporters under N stress, and increased relative abundance of orthologs related to acquisition of inorganic and organic P substrates under P stress. Although the global transcriptional responses were dominated by species-specific changes, the analysis of conserved responses revealed functional similarities in resource acquisition pathways among different phytoplankton taxa. This overlap in nutrient stress responses observed among species may be useful for tracking the physiological ecology of phytoplankton field populations.
Collapse
Affiliation(s)
- Matthew J Harke
- Lamont-Doherty Earth Observatory, Columbia UniversityPalisades, NY, United States
| | - Andrew R Juhl
- Lamont-Doherty Earth Observatory, Columbia UniversityPalisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia UniversityPalisades, NY, United States
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Columbia UniversityPalisades, NY, United States
| | - Harriet Alexander
- Department of Population Health and Reproduction, University of California, DavisDavis, CA, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia UniversityPalisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia UniversityPalisades, NY, United States
| |
Collapse
|
29
|
Liu Z, Campbell V, Heidelberg KB, Caron DA. Gene expression characterizes different nutritional strategies among three mixotrophic protists. FEMS Microbiol Ecol 2016; 92:fiw106. [PMID: 27194617 DOI: 10.1093/femsec/fiw106] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2016] [Indexed: 12/16/2022] Open
Abstract
Mixotrophic protists, i.e. protists that can carry out both phototrophy and heterotrophy, are a group of organisms with a wide range of nutritional strategies. The ecological and biogeochemical importance of these species has recently been recognized. In this study, we investigated and compared the gene expression of three mixotrophic protists, Prymnesium parvum, Dinobyron sp. and Ochromonas sp. under light and dark conditions in the presence of prey using RNA-Seq. Gene expression of the obligately phototrophic P. parvum and Dinobryon sp. changed significantly between light and dark treatments, while that of primarily heterotrophic Ochromonas sp. was largely unchanged. Gene expression of P. parvum and Dinobryon sp. shared many similarities, especially in the expression patterns of genes related to reproduction. However, key genes involved in central carbon metabolism and phagotrophy had different expression patterns between these two species, suggesting differences in prey consumption and heterotrophic nutrition in the dark. Transcriptomic data also offered clues to other physiological traits of these organisms such as preference of nitrogen sources and photo-oxidative stress. These results provide potential target genes for further exploration of the mechanisms of mixotrophic physiology and demonstrate the potential usefulness of molecular approaches in characterizing the nutritional modes of mixotrophic protists.
Collapse
Affiliation(s)
- Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA
| | - Victoria Campbell
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA
| | - Karla B Heidelberg
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA
| |
Collapse
|