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Nejamkin A, Del Castello F, Lamattina L, Foresi N, Correa Aragunde N. Redox regulation in primary nitrate response: Nitric oxide in the spotlight. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108625. [PMID: 38643539 DOI: 10.1016/j.plaphy.2024.108625] [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: 12/01/2023] [Revised: 03/02/2024] [Accepted: 04/09/2024] [Indexed: 04/23/2024]
Abstract
Nitrogen (N) is the main macronutrient of plants that determines growth and productivity. Nitrate is the major source form of N in soils and its uptake and assimilatory pathway has been extensively studied. The early events that occur after the perception of nitrate is known as primary nitrate response (PNR). In this review, new findings on the redox signal that impacts PNR are discussed. We will focus on the novel role of Nitric Oxide (NO) as a signal molecule and the mechanisms that are involved to control NO homeostasis during PNR. Moreover, the role of Reactive Oxygen Species (ROS) and the possible interplay with NO in the PNR are discussed. The sources of NO during PNR will be analyzed as well as the regulation of its intracellular levels. Furthermore, we explored the relevance of the direct action of NO through the S-nitrosation of the transcription factor NLP7, one of the master regulators in the nitrate signaling cascade. This review gives rise to an interesting field with new actors to mark future research directions. This allows us to increase the knowledge of the physiological and molecular fine-tuned modulation during nitrate signaling processes in plants. The discussion of new experimental data will stimulate efforts to further refine our understanding of the redox regulation of nitrate signaling.
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Affiliation(s)
- Andrés Nejamkin
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar Del Plata, Argentina
| | - Fiorella Del Castello
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar Del Plata, Argentina
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar Del Plata, Argentina
| | - Noelia Foresi
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar Del Plata, Argentina
| | - Natalia Correa Aragunde
- Instituto de Investigaciones Biológicas-CONICET, Universidad Nacional de Mar Del Plata, Argentina.
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2
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Xiao J, Zhou Y, Xie Y, Li T, Su X, He J, Jiang Y, Zhu H, Qu H. ATP homeostasis and signaling in plants. PLANT COMMUNICATIONS 2024; 5:100834. [PMID: 38327057 PMCID: PMC11009363 DOI: 10.1016/j.xplc.2024.100834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/14/2024] [Accepted: 02/03/2024] [Indexed: 02/09/2024]
Abstract
ATP is the primary form of energy for plants, and a shortage of cellular ATP is generally acknowledged to pose a threat to plant growth and development, stress resistance, and crop quality. The overall metabolic processes that contribute to the ATP pool, from production, dissipation, and transport to elimination, have been studied extensively. Considerable evidence has revealed that in addition to its role in energy supply, ATP also acts as a regulatory signaling molecule to activate global metabolic responses. Identification of the eATP receptor DORN1 contributed to a better understanding of how plants cope with disruption of ATP homeostasis and of the key points at which ATP signaling pathways intersect in cells or whole organisms. The functions of SnRK1α, the master regulator of the energy management network, in restoring the equilibrium of the ATP pool have been demonstrated, and the vast and complex metabolic network mediated by SnRK1α to adapt to fluctuating environments has been characterized. This paper reviews recent advances in understanding the regulatory control of the cellular ATP pool and discusses possible interactions among key regulators of ATP-pool homeostasis and crosstalk between iATP/eATP signaling pathways. Perception of ATP deficit and modulation of cellular ATP homeostasis mediated by SnRK1α in plants are discussed at the physiological and molecular levels. Finally, we suggest future research directions for modulation of plant cellular ATP homeostasis.
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Affiliation(s)
- Jiaqi Xiao
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijie Zhou
- Guangdong AIB Polytechnic, Guangzhou 510507, China
| | - Yunyun Xie
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Taotao Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinguo Su
- Guangdong AIB Polytechnic, Guangzhou 510507, China
| | - Junxian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hongxia Qu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Zhang X, Yu K, Li M, Jiang H, Gao W, Zhao J, Li K. Diatom-dinoflagellate succession in the Bohai Sea: The role of N/P ratios and dissolved organic nitrogen components. WATER RESEARCH 2024; 251:121150. [PMID: 38246079 DOI: 10.1016/j.watres.2024.121150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Dissolved organic nitrogen (DON) is a pivotal component of total dissolved nitrogen pools, serving as a crucial nitrogen source for phytoplankton. This study investigated the impact of nitrogen-to-phosphorus (N/P) ratios and different DON components (hydrophilic vs hydrophobic DON) on diatom-dinoflagellate succession through field culture experiments. Results showed that dinoflagellates have a competitive advantage under high N/P ratios and phosphorus limitation, regardless of DON or DIN treatments. Hydrophilic DON exhibits greater bioavailability than hydrophobic DON (40.6% vs. 21.7 %), resulting in increased algal biomass and diatoms dominance in the community. Additionally, DON was categorized into labile and refractory components (LDON and RDON) based on bioavailability. LDON primarily consists of protein-like components that can be readily consumed by algae, whereas RDON is primarily composed of humic-like components that are less accessible to algae. Diatoms and dinoflagellates exhibited differential responses to LDON and RDON, with diatoms thriving in high LDON environments, while dinoflagellates gained a competitive advantage when RDON was the predominant nitrogen source. Furthermore, a significant negative correlation was observed between bioavailable nitrogen concentration (BAN: DIN + LDON) and the ratio of dinoflagellates to diatoms (p<0.05). In conclusion, our study highlights the role of LDON in promoting diatom dominance, whereas environments dominated by RDON foster dinoflagellate success. These findings enhance our comprehension of diatom-dinoflagellate succession dynamics.
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Affiliation(s)
- Xiansheng Zhang
- Key Laboratory of Marine Chemistry Theory and Technology, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 2066061, China
| | - Kunlong Yu
- Key Laboratory of Marine Chemistry Theory and Technology, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 2066061, China
| | - Min Li
- Key Laboratory of Marine Chemistry Theory and Technology, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 2066061, China
| | - Heng Jiang
- Key Laboratory of Marine Chemistry Theory and Technology, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 2066061, China
| | - Weimin Gao
- Key Laboratory of Marine Chemistry Theory and Technology, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 2066061, China
| | - Jing Zhao
- Key Laboratory of Marine Chemistry Theory and Technology, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao 266100, China
| | - Keqiang Li
- Key Laboratory of Marine Chemistry Theory and Technology, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 2066061, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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4
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Santin A, Russo MT, de Los Ríos LM, Chiurazzi M, d'Alcalà MR, Lacombe B, Ferrante MI, Rogato A. The tonoplast localized protein PtNPF1 participates in the regulation of nitrogen response in diatoms. THE NEW PHYTOLOGIST 2024; 241:1592-1604. [PMID: 38084038 DOI: 10.1111/nph.19461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
Diatoms are a highly successful group of phytoplankton, well adapted also to oligotrophic environments and capable of handling nutrient fluctuations in the ocean, particularly nitrate. The presence of a large vacuole is an important trait contributing to their adaptive features. It confers diatoms the ability to accumulate and store nutrients, such as nitrate, when they are abundant outside and then to reallocate them into the cytosol to meet deficiencies, in a process called luxury uptake. The molecular mechanisms that regulate these nitrate fluxes are still not known in diatoms. In this work, we provide new insights into the function of Phaeodactylum tricornutum NPF1, a putative low-affinity nitrate transporter. To accomplish this, we generated overexpressing strains and CRISPR/Cas9 loss-of-function mutants. Microscopy observations confirmed predictions that PtNPF1 is localized on the vacuole membrane. Furthermore, functional characterizations performed on knock-out mutants revealed a transient growth delay phenotype linked to altered nitrate uptake. Together, these results allowed us to hypothesize that PtNPF1 is presumably involved in modulating intracellular nitrogen fluxes, managing intracellular nutrient availability. This ability might allow diatoms to fine-tune the assimilation, storage and reallocation of nitrate, conferring them a strong advantage in oligotrophic environments.
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Affiliation(s)
- Anna Santin
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | | | - Laura Morales de Los Ríos
- Institute for Plant Science of Montpellier (IPSiM), University of Montpellier, CNRS, INRAE, Montpellier SupAgro, Place Pierre Viala 2, Montpellier, 34060, France
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, 80131, Italy
| | | | - Benoît Lacombe
- Institute for Plant Science of Montpellier (IPSiM), University of Montpellier, CNRS, INRAE, Montpellier SupAgro, Place Pierre Viala 2, Montpellier, 34060, France
| | - Maria Immacolata Ferrante
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
- National Institute of Oceanography and Applied Geophysics, Trieste, 34010, Italy
| | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, Naples, 80131, Italy
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5
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Pan Y, Zhang W, Wang X, Jouhet J, Maréchal E, Liu J, Xia XQ, Hu H. Allele-dependent expression and functionality of lipid enzyme phospholipid:diacylglycerol acyltransferase affect diatom carbon storage and growth. PLANT PHYSIOLOGY 2024; 194:1024-1040. [PMID: 37930282 DOI: 10.1093/plphys/kiad581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/06/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
In the acyl-CoA-independent pathway of triacylglycerol (TAG) synthesis unique to plants, fungi, and algae, TAG formation is catalyzed by the enzyme phospholipid:diacylglycerol acyltransferase (PDAT). The unique PDAT gene of the model diatom Phaeodactylum tricornutum strain CCMP2561 boasts 47 single nucleotide variants within protein coding regions of the alleles. To deepen our understanding of TAG synthesis, we observed the allele-specific expression of PDAT by the analysis of 87 published RNA-sequencing (RNA-seq) data and experimental validation. The transcription of one of the two PDAT alleles, Allele 2, could be specifically induced by decreasing nitrogen concentrations. Overexpression of Allele 2 in P. tricornutum substantially enhanced the accumulation of TAG by 44% to 74% under nutrient stress; however, overexpression of Allele 1 resulted in little increase of TAG accumulation. Interestingly, a more serious growth inhibition was observed in the PDAT Allele 1 overexpression strains compared with Allele 2 counterparts. Heterologous expression in yeast (Saccharomyces cerevisiae) showed that enzymes encoded by PDAT Allele 2 but not Allele 1 had TAG biosynthetic activity, and 7 N-terminal and 3 C-terminal amino acid variants between the 2 allele-encoded proteins substantially affected enzymatic activity. P. tricornutum PDAT, localized in the innermost chloroplast membrane, used monogalactosyldiacylglycerol and phosphatidylcholine as acyl donors as demonstrated by the increase of the 2 lipids in PDAT knockout lines, which indicated a common origin in evolution with green algal PDATs. Our study reveals unequal roles among allele-encoded PDATs in mediating carbon storage and growth in response to nitrogen stress and suggests an unsuspected strategy toward lipid and biomass improvement for biotechnological purposes.
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Affiliation(s)
- Yufang Pan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiaofei Wang
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, Grenoble Cedex 9 38054, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, Grenoble Cedex 9 38054, France
| | - Jin Liu
- Laboratory for Algae Biotechnology and Innovation, College of Engineering, Peking University, Beijing 100871, China
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanhua Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Huang T, Pan Y, Maréchal E, Hu H. Proteomes reveal the lipid metabolic network in the complex plastid of Phaeodactylum tricornutum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:385-403. [PMID: 37733835 DOI: 10.1111/tpj.16477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Abstract
Phaeodactylum tricornutum plastid is surrounded by four membranes, and its protein composition and function remain mysterious. In this study, the P. tricornutum plastid-enriched fraction was obtained and 2850 proteins were identified, including 92 plastid-encoded proteins, through label-free quantitative proteomic technology. Among them, 839 nuclear-encoded proteins were further determined to be plastidial proteins based on the BLAST alignments within Plant Proteome DataBase and subcellular localization prediction, in spite of the strong contamination by mitochondria-encoded proteins and putative plasma membrane proteins. According to our proteomic data, we reconstructed the metabolic pathways and highlighted the hybrid nature of this diatom plastid. Triacylglycerol (TAG) hydrolysis and glycolysis, as well as photosynthesis, glycan metabolism, and tocopherol and triterpene biosynthesis, occur in the plastid. In addition, the synthesis of long-chain acyl-CoAs, elongation, and desaturation of fatty acids (FAs), and synthesis of lipids including TAG are confined in the four-layered-membrane plastid based on the proteomic and GFP-fusion localization data. The whole process of generation of docosahexaenoic acid (22:6) from palmitic acid (16:0), via elongation and desaturation of FAs, occurs in the chloroplast endoplasmic reticulum membrane, the outermost membrane of the plastid. Desaturation that generates 16:4 from 16:0 occurs in the plastid stroma and outer envelope membrane. Quantitative analysis of glycerolipids between whole cells and isolated plastids shows similar composition, and the FA profile of TAG was not different. This study shows that the diatom plastid combines functions usually separated in photosynthetic eukaryotes, and differs from green alga and plant chloroplasts by undertaking the whole process of lipid biosynthesis.
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Affiliation(s)
- Teng Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Université Grenoble Alpes, CEA, CNRS, INRA, IRIG-LPCV, 38054, Grenoble Cedex 9, France
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Glockow T, Velaz Martín M, Meisch L, Kapieske D, Meissner K, Correa Cassal M, Kaster AK, Rabe KS, Niemeyer CM. A photobioreactor for production of algae biomass from gaseous emissions of an animal house. Appl Microbiol Biotechnol 2023; 107:7673-7684. [PMID: 37815614 PMCID: PMC10656320 DOI: 10.1007/s00253-023-12815-7] [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: 09/14/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023]
Abstract
Sustainable approaches to circular economy in animal agriculture are still poorly developed. Here, we report an approach to reduce gaseous emissions of CO2 and NH3 from animal housing while simultaneously using them to produce value-added biomass. To this end, a cone-shaped, helical photobioreactor was developed that can be integrated into animal housing by being freely suspended, thereby combining a small footprint with a physically robust design. The photobioreactor was coupled with the exhaust air of a chicken house to allow continuous cultivation of a mixed culture of Arthrospira spec. (Spirulina). Continuous quantification of CO2 and NH3 concentration showed that the coupled algae reactor effectively purifies the exhaust air from the chicken house while producing algal biomass. Typical production rates of greater than 0.3 g/l*day dry mass were obtained, and continuous operation was possible for several weeks. Morphological, biochemical, and genomic characterization of Spirulina cultures yielded insights into the dynamics and metabolic processes of the microbial community. We anticipate that further optimization of this approach will provide new opportunities for the generation of value-added products from gaseous CO2 and NH3 waste emissions, linking resource-efficient production of microalgae with simultaneous sequestration of animal emissions. KEY POINTS: • Coupling a bioreactor with exhaust gases of chicken coop for production of biomass. • Spirulina mixed culture removes CO2 and NH3 from chicken house emissions. • High growth rates and biodiversity adaptation for nitrogen metabolism. Towards a sustainable circular economy in livestock farming. The functional coupling of a helical tube photobioreactor with exhaust air from a chicken house enabled the efficient cultivation of Spirulina microalgae while simultaneously sequestering the animals' CO2 and NH3 emissions.
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Affiliation(s)
- Till Glockow
- Acheron GmbH, Auf der Muggenburg 30, 28217, Bremen, Germany
| | - Marta Velaz Martín
- Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Laura Meisch
- Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Denis Kapieske
- Acheron GmbH, Auf der Muggenburg 30, 28217, Bremen, Germany
| | - Kai Meissner
- Acheron GmbH, Auf der Muggenburg 30, 28217, Bremen, Germany
| | - Maximiano Correa Cassal
- Institute for Biological Interfaces 5 (IBG-5), Biotechnology and Microbial Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5 (IBG-5), Biotechnology and Microbial Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Kersten S Rabe
- Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Christof M Niemeyer
- Institute for Biological Interfaces 1 (IBG-1), Biomolecular Micro- and Nanostructures, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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8
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Garza EA, Bielinski VA, Espinoza JL, Orlandi K, Alfaro JR, Bolt TM, Beeri K, Weyman PD, Dupont CL. Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering. ACS Synth Biol 2023; 12:3215-3228. [PMID: 37857380 PMCID: PMC10661051 DOI: 10.1021/acssynbio.3c00163] [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: 03/21/2023] [Indexed: 10/21/2023]
Abstract
While diatoms are promising synthetic biology platforms, there currently exists a limited number of validated genetic regulatory parts available for genetic engineering. The standard method for diatom transformation, nonspecific introduction of DNA into chromosomes via biolistic particle bombardment, is low throughput and suffers from clonal variability and epigenetic effects. Recent developments in diatom engineering have demonstrated that autonomously replicating episomal plasmids serve as stable expression platforms for diverse gene expression technologies. These plasmids are delivered via bacterial conjugation and, when combined with modular DNA assembly technologies, provide a flexibility and speed not possible with biolistic-mediated strain generation. In order to expand the current toolbox for plasmid-based engineering in the diatom Phaeodactylum tricornutum, a conjugation-based forward genetics screen for promoter discovery was developed, and application to a diatom genomic DNA library defined 252 P. tricornutum promoter elements. From this library, 40 promoter/terminator pairs were delivered via conjugation on episomal plasmids, characterized in vivo, and ranked across 4 orders of magnitude difference in reporter gene expression levels.
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Affiliation(s)
- Erin A. Garza
- J. Craig Venter Institute, La Jolla, California 92037, United States
| | | | - Josh L. Espinoza
- J. Craig Venter Institute, La Jolla, California 92037, United States
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9
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Fujita H, Ushio M, Suzuki K, Abe MS, Yamamichi M, Okazaki Y, Canarini A, Hayashi I, Fukushima K, Fukuda S, Kiers ET, Toju H. Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics. Front Microbiol 2023; 14:1261137. [PMID: 38033594 PMCID: PMC10684785 DOI: 10.3389/fmicb.2023.1261137] [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: 07/19/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).
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Affiliation(s)
- Hiroaki Fujita
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Masayuki Ushio
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Department of Ocean Science (OCES), The Hong Kong University of Science and Technology (HKUST), Kowloon, Hong Kong SAR, China
| | - Kenta Suzuki
- Integrated Bioresource Information Division, BioResource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Masato S. Abe
- Faculty of Culture and Information Science, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Masato Yamamichi
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Yusuke Okazaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Alberto Canarini
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Ibuki Hayashi
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Keitaro Fukushima
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - E. Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
- Graduate School of Biostudies, Kyoto University, Sakyo, Kyoto, Japan
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10
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Brunson JK, Thukral M, Ryan JP, Anderson CR, Kolody BC, James C, Chavez FP, Leaw CP, Rabines AJ, Venepally P, Zheng H, Kudela RM, Smith GJ, Moore BS, Allen AE. Molecular Forecasting of Domoic Acid during a Pervasive Toxic Diatom Bloom. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.02.565333. [PMID: 37961417 PMCID: PMC10635071 DOI: 10.1101/2023.11.02.565333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In 2015, the largest recorded harmful algal bloom (HAB) occurred in the Northeast Pacific, causing nearly 100 million dollars in damages to fisheries and killing many protected marine mammals. Dominated by the toxic diatom Pseudo-nitzschia australis , this bloom produced high levels of the neurotoxin domoic acid (DA). Through molecular and transcriptional characterization of 52 near-weekly phytoplankton net-tow samples collected at a bloom hotspot in Monterey Bay, California, we identified active transcription of known DA biosynthesis ( dab ) genes from the three identified toxigenic species, including P. australis as the primary origin of toxicity. Elevated expression of silicon transporters ( sit1 ) during the bloom supports the previously hypothesized role of dissolved silica (Si) exhaustion in contributing to bloom physiology and toxicity. We find that co-expression of the dabA and sit1 genes serves as a robust predictor of DA one week in advance, potentially enabling the forecasting of DA-producing HABs. We additionally present evidence that low levels of iron could have co-limited the diatom population along with low Si. Iron limitation represents a previously unrecognized driver of both toxin production and ecological success of the low iron adapted Pseudo-nitzschia genus during the 2015 bloom, and increasing pervasiveness of iron limitation may fuel the escalating magnitude and frequency of toxic Pseudo-nitzschia blooms globally. Our results advance understanding of bloom physiology underlying toxin production, bloom prediction, and the impact of global change on toxic blooms. Significance Pseudo-nitzschia diatoms form oceanic harmful algal blooms that threaten human health through production of the neurotoxin domoic acid (DA). DA biosynthetic gene expression is hypothesized to control DA production in the environment, yet what regulates expression of these genes is yet to be discovered. In this study, we uncovered expression of DA biosynthesis genes by multiple toxigenic Pseudo-nitzschia species during an economically impactful bloom along the North American West Coast, and identified genes that predict DA in advance of its production. We discovered that iron and silica co-limitation restrained the bloom and likely promoted toxin production. This work suggests that increasing iron limitation due to global change may play a previously unrecognized role in driving bloom frequency and toxicity.
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11
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Walworth NG, Espinoza JL, Argyle PA, Hinners J, Levine NM, Doblin MA, Dupont CL, Collins S. Genus-Wide Transcriptional Landscapes Reveal Correlated Gene Networks Underlying Microevolutionary Divergence in Diatoms. Mol Biol Evol 2023; 40:msad218. [PMID: 37874344 PMCID: PMC10595192 DOI: 10.1093/molbev/msad218] [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: 04/28/2023] [Revised: 08/24/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
Marine microbes like diatoms make up the base of marine food webs and drive global nutrient cycles. Despite their key roles in ecology, biogeochemistry, and biotechnology, we have limited empirical data on how forces other than adaptation may drive diatom diversification, especially in the absence of environmental change. One key feature of diatom populations is frequent extreme reductions in population size, which can occur both in situ and ex situ as part of bloom-and-bust growth dynamics. This can drive divergence between closely related lineages, even in the absence of environmental differences. Here, we combine experimental evolution and transcriptome landscapes (t-scapes) to reveal repeated evolutionary divergence within several species of diatoms in a constant environment. We show that most of the transcriptional divergence can be captured on a reduced set of axes, and that repeatable evolution can occur along a single major axis of variation defined by core ortholog expression comprising common metabolic pathways. Previous work has associated specific transcriptional changes in gene networks with environmental factors. Here, we find that these same gene networks diverge in the absence of environmental change, suggesting these pathways may be central in generating phenotypic diversity as a result of both selective and random evolutionary forces. If this is the case, these genes and the functions they encode may represent universal axes of variation. Such axes that capture suites of interacting transcriptional changes during diversification improve our understanding of both global patterns in local adaptation and microdiversity, as well as evolutionary forces shaping algal cultivation.
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Affiliation(s)
- Nathan G Walworth
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
- J.Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Phoebe A Argyle
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Jana Hinners
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Helmholtz-Zentrum Hereon, 21502 Geesthacht, Germany
| | - Naomi M Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-0371, USA
| | - Martina A Doblin
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | | | - Sinéad Collins
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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12
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Sajib SA, Kandel M, Prity SA, Oukacine C, Gakière B, Merendino L. Role of plastids and mitochondria in the early development of seedlings in dark growth conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1272822. [PMID: 37841629 PMCID: PMC10570830 DOI: 10.3389/fpls.2023.1272822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Establishment of the seedlings is a crucial stage of the plant life cycle. The success of this process is essential for the growth of the mature plant. In Nature, when seeds germinate under the soil, seedlings follow a dark-specific program called skotomorphogenesis, which is characterized by small, non-green cotyledons, long hypocotyl, and an apical hook-protecting meristematic cells. These developmental structures are required for the seedlings to emerge quickly and safely through the soil and gain autotrophy before the complete depletion of seed resources. Due to the lack of photosynthesis during this period, the seed nutrient stocks are the primary energy source for seedling development. The energy is provided by the bioenergetic organelles, mitochondria, and etioplast (plastid in the dark), to the cell in the form of ATP through mitochondrial respiration and etio-respiration processes, respectively. Recent studies suggest that the limitation of the plastidial or mitochondrial gene expression induces a drastic reprogramming of the seedling morphology in the dark. Here, we discuss the dark signaling mechanisms involved during a regular skotomorphogenesis and how the dysfunction of the bioenergetic organelles is perceived by the nucleus leading to developmental changes. We also describe the probable involvement of several plastid retrograde pathways and the interconnection between plastid and mitochondria during seedling development. Understanding the integration mechanisms of organellar signals in the developmental program of seedlings can be utilized in the future for better emergence of crops through the soil.
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Affiliation(s)
- Salek Ahmed Sajib
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Margot Kandel
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Sadia Akter Prity
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Cylia Oukacine
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Bertrand Gakière
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Livia Merendino
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
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13
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Mo J, Lv R, Qin X, Wu X, Chen H, Yan N, Shi J, Wu Y, Liu W, Kong RYC, Guo J. Mechanistic insights into hormesis induced by erythromycin in the marine alga Thalassiosira weissflogii. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115242. [PMID: 37441949 DOI: 10.1016/j.ecoenv.2023.115242] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/17/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
Erythromycin (ERY) is a typical macrolide antibiotic with large production and extensive use on a global scale. Detection of ERY in both freshwaters and coaster seawaters, as well as relatively high ecotoxicity of ERY have been documented. Notably, hormesis has been reported on several freshwater algae under ERY stress, where growth was promoted at relatively lower exposures but inhibited at higher treatment levels. On the contrary, there is limited information of ERY toxicity in marine algae, hampering the risk assessment on ERY in the coaster waters. The presence of hormesis may challenge the current concept of dose-response adopted in chemical risk assessment. Whether and how exposure to ERY can induce dose-dependent toxicity in marine algae remain virtually unknown, especially at environmentally relevant concentrations. The present study used a model marine diatom Thalassiosira weissflogii (T. weissflogii) to reveal its toxicological responses to ERY at different biological levels and decipher the underlying mechanisms. Assessment of multiple apical endpoints shows an evident growth promotion following ERY exposure at an environmentally relevant concentration (1 µg/L), associated with increased contents reactive oxygen species (ROS) and chlorophyll-a (Chl-a), activated signaling pathways related to ribosome biosynthesis and translation, and production of total soluble protein. By contrast, growth inhibition in the 750 and 2500 µg/L treatments was attributed to reduced viability, increased ROS formation, reduced content of total soluble protein, inhibited photosynthesis, and perturbed signaling pathways involved in xenobiotic metabolism, ribosome, metabolism of amino acid, and nitrogen metabolism. Measurements of multiple apical endpoints coupled with de novo transcriptomics analysis applied in the present study, a systems biology approach, can generate detailed mechanistic information of chemical toxicity including dose-response and species sensitivity difference used in environmental risk assessment.
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Affiliation(s)
- Jiezhang Mo
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China; State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region.
| | - Runnan Lv
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Xian Qin
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Xintong Wu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Haibo Chen
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Neng Yan
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jingchun Shi
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Yinglin Wu
- School of Life Science and Technology, Lingnan Normal University, Zhanjiang, Guangdong 524048, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Shantou University, Shantou 515063, China
| | - Richard Y C Kong
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
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14
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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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15
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Nwankwegu AS, Yang G, Zhang L, Xie D, Ohore OE, Adeyeye OA, Li Y, Yao X, Song Z, Yonas MW. Ecosystem anthropogenic enrichments enhance Chroococcus abundance and suppress Anabaena during cyanobacterial-dominated spring blooms in the Pengxi River, Three Gorges Reservoir, China. MARINE POLLUTION BULLETIN 2023; 193:115141. [PMID: 37295313 DOI: 10.1016/j.marpolbul.2023.115141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Taxa-specific responses to the increasing anthropogenic eutrophication offer promising insights for mitigating harmful algal blooms (HABs) in freshwaters. The present study evaluated the HABs species dynamics in response to the ecosystem anthropogenic enrichment during cyanobacterial-dominated spring HABs in the Pengxi River, Three Gorges Reservoir, China. Results show significant cyanobacterial dominance with a relative abundance (RA = 76.54 %). The ecosystem enrichments triggered shifts in the HABs community structure from Anabaena to Chroococcus, especially in the culture involving iron (Fe) addition (RA = 66.16 %). While P-alone enrichment caused a dramatic increase in the aggregate cell density (2.45 × 108 cells L-1), the multiple enrichment (NPFe) led to maximum biomass production (as chl-a = 39.62 ± 2.33 μgL-1), indicating that nutrient in conjunction with the HABs taxonomic characteristics e.g., tendency to possess high cell pigment contents rather than cell density can potentially determine massive biomass accumulations during HABs. The stimulation of growth as biomass production demonstrated by both P-alone and the multiple enrichments, NPFe indicates that although P exclusive control is feasible in the Pengxi ecosystem, it can only guarantee a short-term reduction in HABs magnitude and duration, thus a lasting HABs mitigation measure must consider a policy recommendation involving multiple nutrient management, especially N and P dual control strategy. The present study would adequately complement the concerted effort in developing a rational predictive framework for freshwater eutrophication management and HABs mitigations in the TGR and elsewhere with similar anthropogenic stressors.
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Affiliation(s)
- Amechi S Nwankwegu
- College of Resources and Environment, Southwest University, 1 Tiansheng Road, Beibei District, Chongqing 400716, China; National Base of International S&T Collaboration on Water Environmental Monitoring and Simulation in Three Gorges Reservoir Region, Chongqing 400716, China; College of Environment, Hohai University, No.1 Xikang Road, Gulou District, Nanjing 210098, China
| | - Guanglang Yang
- College of Resources and Environment, Southwest University, 1 Tiansheng Road, Beibei District, Chongqing 400716, China
| | - Lei Zhang
- College of Resources and Environment, Southwest University, 1 Tiansheng Road, Beibei District, Chongqing 400716, China; National Base of International S&T Collaboration on Water Environmental Monitoring and Simulation in Three Gorges Reservoir Region, Chongqing 400716, China.
| | - Deti Xie
- College of Resources and Environment, Southwest University, 1 Tiansheng Road, Beibei District, Chongqing 400716, China; National Base of International S&T Collaboration on Water Environmental Monitoring and Simulation in Three Gorges Reservoir Region, Chongqing 400716, China
| | - Okugbe E Ohore
- Institute of Marine Sciences, Shantou University, Shantou 515063, China
| | - Oluwafemi Adewole Adeyeye
- College of Resources and Environment, Southwest University, 1 Tiansheng Road, Beibei District, Chongqing 400716, China; National Base of International S&T Collaboration on Water Environmental Monitoring and Simulation in Three Gorges Reservoir Region, Chongqing 400716, China
| | - Yiping Li
- College of Environment, Hohai University, No.1 Xikang Road, Gulou District, Nanjing 210098, China
| | - Xuexing Yao
- College of Resources and Environment, Southwest University, 1 Tiansheng Road, Beibei District, Chongqing 400716, China
| | - Zenghui Song
- College of Resources and Environment, Southwest University, 1 Tiansheng Road, Beibei District, Chongqing 400716, China
| | - Muhammad W Yonas
- College of Resources and Environment, Southwest University, 1 Tiansheng Road, Beibei District, Chongqing 400716, China
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16
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Daloso DDM, Morais EG, Oliveira E Silva KF, Williams TCR. Cell-type-specific metabolism in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1093-1114. [PMID: 36987968 DOI: 10.1111/tpj.16214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 05/31/2023]
Abstract
Every plant organ contains tens of different cell types, each with a specialized function. These functions are intrinsically associated with specific metabolic flux distributions that permit the synthesis of the ATP, reducing equivalents and biosynthetic precursors demanded by the cell. Investigating such cell-type-specific metabolism is complicated by the mosaic of different cells within each tissue combined with the relative scarcity of certain types. However, techniques for the isolation of specific cells, their analysis in situ by microscopy, or modeling of their function in silico have permitted insight into cell-type-specific metabolism. In this review we present some of the methods used in the analysis of cell-type-specific metabolism before describing what we know about metabolism in several cell types that have been studied in depth; (i) leaf source and sink cells; (ii) glandular trichomes that are capable of rapid synthesis of specialized metabolites; (iii) guard cells that must accumulate large quantities of the osmolytes needed for stomatal opening; (iv) cells of seeds involved in storage of reserves; and (v) the mesophyll and bundle sheath cells of C4 plants that participate in a CO2 concentrating cycle. Metabolism is discussed in terms of its principal features, connection to cell function and what factors affect the flux distribution. Demand for precursors and energy, availability of substrates and suppression of deleterious processes are identified as key factors in shaping cell-type-specific metabolism.
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Affiliation(s)
- Danilo de Menezes Daloso
- Lab Plant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CA, 60451-970, Brazil
| | - Eva Gomes Morais
- Lab Plant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CA, 60451-970, Brazil
| | - Karen Fernanda Oliveira E Silva
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília-DF, 70910-900, Brazil
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17
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Sun S, Hu X, Kang W, Yao M. Combined effects of microplastics and warming enhance algal carbon and nitrogen storage. WATER RESEARCH 2023; 233:119815. [PMID: 36881974 DOI: 10.1016/j.watres.2023.119815] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Algae dominate primary production in groundwater and oceans and play a critical role in global carbon dioxide fixation and climate change but are threatened by ongoing global warming events (such as heatwaves) and increasing microplastic (MP) pollution. However, whether and how ecologically important phytoplankton respond to the combined effects of warming and MPs remain poorly understood. We thus investigated the combined effects of these factors on carbon and nitrogen storage and the mechanisms underlying the alterations in the physiological performance of a model diatom, Phaeodactylum tricornutum, exposed to a warming stressor (25 °C compared with 21 °C) and polystyrene MP acclimation. Although warmer conditions decreased the cell viability, the diatoms subjected to the synergistic effects of MPs and warming showed significant increases in the growth rate (1.10-fold) and nitrogen uptake rate (1.26-fold). Metabolomics and transcriptomic analyses revealed that MPs and warming mainly promoted fatty acid metabolism, the urea cycle, glutamine and glutamate production, and the tricarboxylic acid (TCA) cycle due to an increased level of 2-oxoglutarate, which is the hub of carbon and nitrogen metabolism and accounts for the acquisition and utilization of carbon and nitrogen. Our findings emphasize the nonnegligible effects of MPs and HWs on the algal carbon and nitrogen cycles in waters.
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Affiliation(s)
- Shan Sun
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Mingqi Yao
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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18
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Kang W, Sun S, Hu X. Microplastics trigger the Matthew effect on nitrogen assimilation in marine diatoms at an environmentally relevant concentration. WATER RESEARCH 2023; 233:119762. [PMID: 36841163 DOI: 10.1016/j.watres.2023.119762] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Microplastics (MPs, diameter <5 mm) are widely distributed on Earth, especially in the oceans. Diatoms account for ∼40% of marine primary productivity and affect the global biogeochemical cycles of macroelements. However, the effects of MPs on marine nitrogen cycling remain poorly understood, particularly comparisons between nitrogen-replete and nitrogen-limited conditions. We found that MPs trigger the Matthew effect on nitrogen assimilation in diatoms, where MPs inhibited nitrogen assimilation under nitrogen-limited conditions while enhancing nitrogen metabolism under nitrogen-replete conditions in Phaeodactylum tricornutum. Nitrate reductase (NR) and nitrite reductase (NIR) are upregulated, but nitrate transporter (NRT) and glutamine synthetase (GS) are downregulated by MPs under nitrogen-limited conditions. In contrast, NR, NIR, and GS are all upregulated by MPs under nitrogen-replete conditions. MPs accelerate nitrogen anabolic processes with an increase in the accumulation of carbohydrates by 80.7 ± 7.9% and enhance the activities of key nitrogen-metabolizing enzymes (8.20-44.90%) under nitrogen-replete conditions. In contrast, the abundance of carbohydrates decreases by 22.0-34.4%, and NRT activity is inhibited by 79.0-86.5% in nitrogen-limited algae exposed to MPs. Metabolomic and transcriptomic analyses were performed to further explore the molecular mechanisms of reprogrammed nitrogen assimilation, including carbon metabolism, nitrogen transport and ammonia assimilation. The aforementioned spatial redistribution (e.g., the Matthew effect between nitrogen-replete and -limited conditions) of nitrogen assimilation highlights the potential risks of MP contamination in the ocean.
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Affiliation(s)
- Weilu Kang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Shan Sun
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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19
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Helliwell KE. Emerging trends in nitrogen and phosphorus signalling in photosynthetic eukaryotes. TRENDS IN PLANT SCIENCE 2023; 28:344-358. [PMID: 36372648 DOI: 10.1016/j.tplants.2022.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) and nitrogen (N) are the major nutrients that constrain plant and algal growth in nature. Recent advances in understanding nutrient signalling mechanisms of these organisms have revealed molecular attributes to optimise N and P acquisition. This has illuminated the importance of interplay between N and P regulatory networks, highlighting a need to study synergistic interactions rather than single-nutrient effects. Emerging insights of nutrient signalling in polyphyletic model plants and algae hint that, although core P-starvation signalling components are conserved, distinct mechanisms for P (and N) sensing have arisen. Here, the N and P signalling mechanisms of diverse photosynthetic eukaryotes are examined, drawing parallels and differences between taxa. Future directions to understand their molecular basis, evolution, and ecology are proposed.
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Affiliation(s)
- Katherine E Helliwell
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK; Marine Biological Association, Citadel Hill, Plymouth PL1 2PB, UK.
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20
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Kinoshita K, Ito K, Katayama S. Evaluation of Nitrogen Source Uptake by the Bivalve Nuttallia olivacea Fed with 15N-Labeled Diatoms. Zoolog Sci 2023; 40:19-23. [PMID: 36744706 DOI: 10.2108/zs220032] [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: 03/30/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022]
Abstract
Marine diatoms are an important food resource for bivalves, but few experimental studies have evaluated diatom assimilation by bivalves. We conducted a laboratory experiment to investigate the ability of the suspension-feeding bivalve Nuttallia olivacea to utilize three common diatom species (planktonic diatoms Thalassiosira pseudonana and Skeletonema dohrnii and the benthic diatom Entomoneis paludosa) as food labeled with heavy nitrogen stable isotope (15N) by incubation in medium containing Na15NO3. The percentage of food-derived nitrogen in the organs of the bivalves increased over time, confirming that the bivalves were taking up dietary nitrogen from diatoms. The proportion of food-derived nitrogen from diatoms to bivalves appeared to be higher in planktonic species than in benthic species. However, it is possible that the benthic diatom intake by the bivalves in this study was underestimated because the substrate was not disturbed as would occur under field conditions. The percentage of food-derived nitrogen in bivalve organs tended to be highest in the digestive diverticula, followed by the foot, mantle, and siphon, regardless of diatom type. These findings suggest that N. olivacea may preferentially distribute nitrogen to organs other than the siphon, which is prone to continuous loss by fish predation.
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Affiliation(s)
- Kyoko Kinoshita
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8572, Japan,
| | - Kinuko Ito
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8572, Japan
| | - Satoshi Katayama
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8572, Japan
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21
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Brownlee C, Helliwell KE, Meeda Y, McLachlan D, Murphy EA, Wheeler GL. Regulation and integration of membrane transport in marine diatoms. Semin Cell Dev Biol 2023; 134:79-89. [PMID: 35305902 DOI: 10.1016/j.semcdb.2022.03.006] [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: 11/25/2021] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 12/27/2022]
Abstract
Diatoms represent one of the most successful groups of marine phytoplankton and are major contributors to ocean biogeochemical cycling. They have colonized marine, freshwater and ice environments and inhabit all regions of the World's oceans, from poles to tropics. Their success is underpinned by a remarkable ability to regulate their growth and metabolism during nutrient limitation and to respond rapidly when nutrients are available. This requires precise regulation of membrane transport and nutrient acquisition mechanisms, integration of nutrient sensing mechanisms and coordination of different transport pathways. This review outlines transport mechanisms involved in acquisition of key nutrients (N, C, P, Si, Fe) by marine diatoms, illustrating their complexity, sophistication and multiple levels of control.
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Affiliation(s)
- Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Ocean and Earth Sciences, University of Southampton, Southampton SO14 3ZH, UK
| | - Katherine E Helliwell
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
| | - Yasmin Meeda
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Deirdre McLachlan
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Eleanor A Murphy
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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22
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He C, Berkowitz O, Hu S, Zhao Y, Qian K, Shou H, Whelan J, Wang Y. Co-regulation of mitochondrial and chloroplast function: Molecular components and mechanisms. PLANT COMMUNICATIONS 2023; 4:100496. [PMID: 36435968 PMCID: PMC9860188 DOI: 10.1016/j.xplc.2022.100496] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
The metabolic interdependence, interactions, and coordination of functions between chloroplasts and mitochondria are established and intensively studied. However, less is known about the regulatory components that control these interactions and their responses to external stimuli. Here, we outline how chloroplastic and mitochondrial activities are coordinated via common components involved in signal transduction pathways, gene regulatory events, and post-transcriptional processes. The endoplasmic reticulum emerges as a point of convergence for both transcriptional and post-transcriptional pathways that coordinate chloroplast and mitochondrial functions. Although the identification of molecular components and mechanisms of chloroplast and mitochondrial signaling increasingly suggests common players, this raises the question of how these allow for distinct organelle-specific downstream pathways. Outstanding questions with respect to the regulation of post-transcriptional pathways and the cell and/or tissue specificity of organelle signaling are crucial for understanding how these pathways are integrated at a whole-plant level to optimize plant growth and its response to changing environmental conditions.
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Affiliation(s)
- Cunman He
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Shanshan Hu
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, P.R. China
| | - Yang Zhao
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Kun Qian
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Huixia Shou
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, P.R. China
| | - James Whelan
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia; International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, Zhejiang 314400, P.R. China
| | - Yan Wang
- College of Life Science, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China; Department of Animal, Plant and Soil Science, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, VIC 3086, Australia.
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NmrA acts as a positive regulator of nitrate assimilation in Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Tan YH, Poong SW, Yang CH, Lim PE, John B, Pai TW, Phang SM. Transcriptomic analysis reveals distinct mechanisms of adaptation of a polar picophytoplankter under ocean acidification conditions. MARINE ENVIRONMENTAL RESEARCH 2022; 182:105782. [PMID: 36308800 DOI: 10.1016/j.marenvres.2022.105782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Human emissions of carbon dioxide are causing irreversible changes in our oceans and impacting marine phytoplankton, including a group of small green algae known as picochlorophytes. Picochlorophytes grown in natural phytoplankton communities under future predicted levels of carbon dioxide have been demonstrated to thrive, along with redistribution of the cellular metabolome that enhances growth rate and photosynthesis. Here, using next-generation sequencing technology, we measured levels of transcripts in a picochlorophyte Chlorella, isolated from the sub-Antarctic and acclimated under high and current ambient CO2 levels, to better understand the molecular mechanisms involved with its ability to acclimate to elevated CO2. Compared to other phytoplankton taxa that induce broad transcriptomic responses involving multiple parts of their cellular metabolism, the changes observed in Chlorella focused on activating gene regulation involved in different sets of pathways such as light harvesting complex binding proteins, amino acid synthesis and RNA modification, while carbon metabolism was largely unaffected. Triggering a specific set of genes could be a unique strategy of small green phytoplankton under high CO2 in polar oceans.
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Affiliation(s)
- Yong-Hao Tan
- Institute for Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia; Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Sze-Wan Poong
- Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia
| | - Cing-Han Yang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Phaik-Eem Lim
- Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia.
| | - Beardall John
- School of Biological Sciences, Monash University, Clayton, Australia
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan; Department of Computer Science and Information Engineering, National Taipei University of Technology, Taipei, Taiwan
| | - Siew-Moi Phang
- Institute of Ocean & Earth Sciences, University of Malaya, Kuala Lumpur, Malaysia; Department of Biotechnology, Faculty of Applied Science, UCSI University, Kuala Lumpur, Malaysia; The Chancellery, UCSI University, Kuala Lumpur, Malaysia
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25
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Biswas H. A story of resilience: Arctic diatom Chaetoceros gelidus exhibited high physiological plasticity to changing CO 2 and light levels. FRONTIERS IN PLANT SCIENCE 2022; 13:1028544. [PMID: 36438134 PMCID: PMC9692007 DOI: 10.3389/fpls.2022.1028544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Arctic phytoplankton are experiencing multifaceted stresses due to climate warming, ocean acidification, retreating sea ice, and associated changes in light availability, and that may have large ecological consequences. Multiple stressor studies on Arctic phytoplankton, particularly on the bloom-forming species, may help understand their fitness in response to future climate change, however, such studies are scarce. In the present study, a laboratory experiment was conducted on the bloom-forming Arctic diatom Chaetoceros gelidus (earlier C. socialis) under variable CO2 (240 and 900 µatm) and light (50 and 100 µmol photons m-2 s-1) levels. The growth response was documented using the pre-acclimatized culture at 2°C in a closed batch system over 12 days until the dissolved inorganic nitrogen was depleted. Particulate organic carbon and nitrogen (POC and PON), pigments, cell density, and the maximum quantum yield of photosystem II (Fv/Fm) were measured on day 4 (D4), 6 (D6), 10 (D10), and 12 (D12). The overall growth response suggested that C. gelidus maintained a steady-state carboxylation rate with subsequent conversion to macromolecules as reflected in the per-cell POC contents under variable CO2 and light levels. A substantial amount of POC buildup at the low CO2 level (comparable to the high CO2 treatment) indicated the possibility of existing carbon dioxide concentration mechanisms (CCMs) that needs further investigation. Pigment signatures revealed a high level of adaptability to variable irradiance in this species without any major CO2 effect. PON contents per cell increased initially but decreased irrespective of CO2 levels when nitrogen was limited (D6 onward) possibly to recycle intracellular nitrogen resources resulting in enhanced C: N ratios. On D12 the decreased dissolved organic nitrogen levels could be attributed to consumption under nitrogen starvation. Such physiological plasticity could make C. gelidus "ecologically resilient" in the future Arctic.
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Affiliation(s)
- Haimanti Biswas
- National Institute of Oceanography - CSIR (Council of Scientific and Industrial Research), Biological Oceanography Division, Goa, India
- Polar Biological Oceanography, Alfred Wegener Institute of Polar and Marine Research, Bremerhaven, Germany
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26
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Li J, Zhang K, Li L, Wang Y, Lin S. Unsuspected functions of alkaline phosphatase PhoD in the diatom Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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27
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Nitrogen and Iron Availability Drive Metabolic Remodeling and Natural Selection of Diverse Phytoplankton during Experimental Upwelling. mSystems 2022; 7:e0072922. [PMID: 36036504 PMCID: PMC9599627 DOI: 10.1128/msystems.00729-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nearly half of carbon fixation and primary production originates from marine phytoplankton, and much of it occurs in episodic blooms in upwelling regimes. Here, we simulated blooms limited by nitrogen and iron by incubating Monterey Bay surface waters with subnutricline waters and inorganic nutrients and measured the whole-community transcriptomic response during mid- and late-bloom conditions. Cell counts revealed that centric and pennate diatoms (largely Pseudo-nitzschia and Chaetoceros spp.) were the major blooming taxa, but dinoflagellates, prasinophytes, and prymnesiophytes also increased. Viral mRNA significantly increased in late bloom and likely played a role in the bloom's demise. We observed conserved shifts in the genetic similarity of phytoplankton populations to cultivated strains, indicating adaptive population-level changes in community composition. Additionally, the density of single nucleotide variants (SNVs) declined in late-bloom samples for most taxa, indicating a loss of intraspecific diversity as a result of competition and a selective sweep of adaptive alleles. We noted differences between mid- and late-bloom metabolism and differential regulation of light-harvesting complexes (LHCs) under nutrient stress. While most LHCs are diminished under nutrient stress, we showed that diverse taxa upregulated specialized, energy-dissipating LHCs in low iron. We also suggest the relative expression of NRT2 compared to the expression of GSII as a marker of cellular nitrogen status and the relative expression of iron starvation-induced protein genes (ISIP1, ISIP2, and ISIP3) compared to the expression of the thiamine biosynthesis gene (thiC) as a marker of iron status in natural diatom communities. IMPORTANCE Iron and nitrogen are the nutrients that most commonly limit phytoplankton growth in the world's oceans. The utilization of these resources by phytoplankton sets the biomass available to marine systems and is of particular interest in high-nutrient, low-chlorophyll (HNLC) coastal fisheries. Previous research has described the biogeography of phytoplankton in HNLC regions and the transcriptional responses of representative taxa to nutrient limitation. However, the differential transcriptional responses of whole phytoplankton communities to iron and nitrogen limitation has not been previously described, nor has the selective pressure that these competitive bloom environments exert on major players. In addition to describing changes in the physiology of diverse phytoplankton, we suggest practical indicators of cellular nitrogen and iron status for future monitoring.
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28
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Zhang SF, Han BB, Shi RJ, Wu FX, Rao YY, Dai M, Huang HH. Quantitative Proteomic Analysis Reveals the Key Molecular Events Driving Phaeocystis globosa Bloom and Dissipation. Int J Mol Sci 2022; 23:ijms232012668. [PMID: 36293526 PMCID: PMC9604223 DOI: 10.3390/ijms232012668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/06/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Phaeocystis globosa is a marine-bloom-forming haptophyte with a polymorphic life cycle alternating between free-living cells and a colonial morphotype, that produces high biomass and impacts ecological structure and function. The mechanisms of P. globosa bloom formation have been extensively studied, and various environmental factors are believed to trigger these events. However, little is known about the intrinsic biological processes that drive the bloom process, and the mechanisms underlying P. globosa bloom formation remain enigmatic. Here, we investigated a P. globosa bloom occurring along the Chinese coast and compared the proteomes of in situ P. globosa colonies from bloom and dissipation phases using a tandem mass tag (TMT)-based quantitative proteomic approach. Among the 5540 proteins identified, 191 and 109 proteins displayed higher abundances in the bloom and dissipation phases, respectively. The levels of proteins involved in photosynthesis, pigment metabolism, nitrogen metabolism, and matrix substrate biosynthesis were distinctly different between these two phases. Ambient nitrate is a key trigger of P. globosa bloom formation, while the enhanced light harvest and multiple inorganic carbon-concentrating mechanisms support the prosperousness of colonies in the bloom phase. Additionally, colonies in the bloom phase have greater carbon fixation potential, with more carbon and energy being fixed and flowing toward the colonial matrix biosynthesis. Our study revealed the key biological processes underlying P. globosa blooms and provides new insights into the mechanisms behind bloom formation.
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Affiliation(s)
- Shu-Fei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Bei-Bei Han
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Rong-Jun Shi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Feng-Xia Wu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Yi-Yong Rao
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Ming Dai
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Hong-Hui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511485, China
- Correspondence:
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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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30
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You Y, Sun X, Ma M, He J, Li L, Porto FW, Lin S. Trypsin is a coordinate regulator of N and P nutrients in marine phytoplankton. Nat Commun 2022; 13:4022. [PMID: 35821503 PMCID: PMC9276738 DOI: 10.1038/s41467-022-31802-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 07/05/2022] [Indexed: 11/30/2022] Open
Abstract
Trypsin is best known as a digestive enzyme in animals, but remains unexplored in phytoplankton, the major primary producers in the ocean. Here we report the prevalence of trypsin genes in global ocean phytoplankton and significant influences of environmental nitrogen (N) and phosphorus (P) on their expression. Using CRISPR/Cas9 mediated-knockout and overexpression analyses, we further reveal that a trypsin in Phaeodactylum tricornutum (PtTryp2) functions to repress N acquisition, but its expression decreases under N-deficiency to promote N acquisition. On the contrary, PtTryp2 promotes phosphate uptake per se, and its expression increases under P-deficiency to further reinforce P acquisition. Furthermore, PtTryp2 knockout led to amplitude magnification of the nitrate and phosphate uptake ‘seesaw’, whereas PtTryp2 overexpression dampened it, linking PtTryp2 to stabilizing N:P stoichiometry. Our data demonstrate that PtTryp2 is a coordinate regulator of N:P stoichiometric homeostasis. The study opens a window for deciphering how phytoplankton adapt to nutrient-variable marine environments. Using CRISPR-Cas9 mediated-knockout and overexpression analyses, this study shows that a trypsin in the diatom Phaeodactylum tricornutum promotes phosphorus uptake and inhibits nitrogen uptake but its expression is downregulated under nitrogen stress and upregulated under phosphorus stress. Together, the findings suggest this trypsin is a coordinate regulator of nutrient homeostasis.
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Affiliation(s)
- Yanchun You
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Minglei Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jiamin He
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Felipe Wendt Porto
- Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China. .,Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA.
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31
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Maniscalco MA, Brzezinski MA, Lampe RH, Cohen NR, McNair HM, Ellis KA, Brown M, Till CP, Twining BS, Bruland KW, Marchetti A, Thamatrakoln K. Diminished carbon and nitrate assimilation drive changes in diatom elemental stoichiometry independent of silicification in an iron-limited assemblage. ISME COMMUNICATIONS 2022; 2:57. [PMID: 37938259 PMCID: PMC9723790 DOI: 10.1038/s43705-022-00136-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/12/2022] [Accepted: 06/09/2022] [Indexed: 06/17/2023]
Abstract
In the California Current Ecosystem, upwelled water low in dissolved iron (Fe) can limit phytoplankton growth, altering the elemental stoichiometry of the particulate matter and dissolved macronutrients. Iron-limited diatoms can increase biogenic silica (bSi) content >2-fold relative to that of particulate organic carbon (C) and nitrogen (N), which has implications for carbon export efficiency given the ballasted nature of the silica-based diatom cell wall. Understanding the molecular and physiological drivers of this altered cellular stoichiometry would foster a predictive understanding of how low Fe affects diatom carbon export. In an artificial upwelling experiment, water from 96 m depth was incubated shipboard and left untreated or amended with dissolved Fe or the Fe-binding siderophore desferrioxamine-B (+DFB) to induce Fe-limitation. After 120 h, diatoms dominated the communities in all treatments and displayed hallmark signatures of Fe-limitation in the +DFB treatment, including elevated particulate Si:C and Si:N ratios. Single-cell, taxon-resolved measurements revealed no increase in bSi content during Fe-limitation despite higher transcript abundance of silicon transporters and silicanin-1. Based on these findings we posit that the observed increase in bSi relative to C and N was primarily due to reductions in C fixation and N assimilation, driven by lower transcript expression of key Fe-dependent genes.
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Affiliation(s)
- Michael A Maniscalco
- Marine Science Institute and The Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
| | - Mark A Brzezinski
- Marine Science Institute and The Department of Ecology Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Robert H Lampe
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, Savannah, GA, USA
| | - Heather M McNair
- University of Rhode Island, Graduate School of Oceanography, Narragansett, RI, USA
| | - Kelsey A Ellis
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | | | - Claire P Till
- Chemistry Department, California State Polytechnic University, Humboldt, Arcata, CA, USA
| | | | - Kenneth W Bruland
- Department of Ocean Sciences, University of California, Santa Cruz, CA, USA
| | - Adrian Marchetti
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, USA
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Pinseel E, Nakov T, Van den Berge K, Downey KM, Judy KJ, Kourtchenko O, Kremp A, Ruck EC, Sjöqvist C, Töpel M, Godhe A, Alverson AJ. Strain-specific transcriptional responses overshadow salinity effects in a marine diatom sampled along the Baltic Sea salinity cline. THE ISME JOURNAL 2022; 16:1776-1787. [PMID: 35383290 PMCID: PMC9213524 DOI: 10.1038/s41396-022-01230-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 05/01/2023]
Abstract
The salinity gradient separating marine and freshwater environments represents a major ecological divide for microbiota, yet the mechanisms by which marine microbes have adapted to and ultimately diversified in freshwater environments are poorly understood. Here, we take advantage of a natural evolutionary experiment: the colonization of the brackish Baltic Sea by the ancestrally marine diatom Skeletonema marinoi. To understand how diatoms respond to low salinity, we characterized transcriptomic responses of acclimated S. marinoi grown in a common garden. Our experiment included eight strains from source populations spanning the Baltic Sea salinity cline. Gene expression analysis revealed that low salinities induced changes in the cellular metabolism of S. marinoi, including upregulation of photosynthesis and storage compound biosynthesis, increased nutrient demand, and a complex response to oxidative stress. However, the strain effect overshadowed the salinity effect, as strains differed significantly in their response, both regarding the strength and the strategy (direction of gene expression) of their response. The high degree of intraspecific variation in gene expression observed here highlights an important but often overlooked source of biological variation associated with how diatoms respond to environmental change.
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Affiliation(s)
- Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.
| | - Teofil Nakov
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Koen Van den Berge
- Department of Statistics, University of California, Berkeley, CA, USA
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Kathryn J Judy
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Olga Kourtchenko
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anke Kremp
- Leibniz-Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Conny Sjöqvist
- Environmental and Marine Biology, Åbo Akademi University, Åbo, Finland
| | - Mats Töpel
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.
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Sun J, Yang L, Xiao S, Chu H, Jiang S, Yu Z, Zhou X, Zhang Y. A promising microalgal wastewater cyclic cultivation technology: Dynamic simulations, economic viability, and environmental suitability. WATER RESEARCH 2022; 217:118411. [PMID: 35429879 DOI: 10.1016/j.watres.2022.118411] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/22/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
The microalgal wastewater cyclic cultivation technology (AWC2T) proposed in this study helps address the challenges surrounding water scarcity and ecological sustainability in a clean, resource-efficient, and affordable manner. A novel microalgae growth model (AGM) elucidating the growth mechanisms of microalgae in the AWC2T system was established for dynamic simulations and design optimization. The recycled wastewater accelerated the growth rate of microalgae, and increased biomass and lipids content by 11% and 37.65%, respectively, after 8 batches of cultivation. The accumulated soluble algae products (SAPs) enhanced microalgae growth by providing nutrients and regulating metabolism. In addition, scenario simulations illustrated the excellent long-term performance of the AWC2T system. 100% recycling of microalgal wastewater could save 0.3% N and 54.36% P. The techno-economic analysis (TEA) and life cycle assessment (LCA) explored how economic and sustainability principles can be embedded into the life cycle of microalgae production. The AWC2T led to outcomes vastly superior to non-cyclic technology by enabling the high-level recovery of resources, providing substantial benefits, enhancing contingency and risk resistance, and offsetting a host of unintended environmental effects.
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Affiliation(s)
- Jingjing Sun
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Libin Yang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Shaoze Xiao
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Huaqiang Chu
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; Shanghai Institute of pollution control and ecological security, Tongji University, Shanghai 200092, China.
| | - Shuhong Jiang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Zhenjiang Yu
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Xuefei Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; Shanghai Institute of pollution control and ecological security, Tongji University, Shanghai 200092, China.
| | - Yalei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China; Shanghai Institute of pollution control and ecological security, Tongji University, Shanghai 200092, China.
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Perera IA, Abinandan S, Subashchandrabose SR, Venkateswarlu K, Naidu R, Megharaj M. Impact of Nitrate and Ammonium Concentrations on Co-Culturing of Tetradesmus obliquus IS2 with Variovorax paradoxus IS1 as Revealed by Phenotypic Responses. MICROBIAL ECOLOGY 2022; 83:951-959. [PMID: 34363515 DOI: 10.1007/s00248-021-01832-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Mutual interactions in co-cultures of microalgae and bacteria are well known for establishing consortia and nutrient uptake in aquatic habitats, but the phenotypic changes in terms of morphological, physiological, and biochemical attributes that drive these interactions have not been clearly understood. In this novel study, we demonstrated the phenotypic response in a co-culture involving a microalga, Tetradesmus obliquus IS2, and a bacterium, Variovorax paradoxus IS1, grown with varying concentrations of two inorganic nitrogen sources. Modified Bold's basal medium was supplemented with five ratios (%) of NO3-N:NH4-N (100:0, 75:25, 50:50, 25:75, and 0:100), and by maintaining N:P Redfield ratio of 16:1. The observed morphological changes in microalga included an increase in granularity and a broad range of cell sizes under the influence of increased ammonium levels. Co-culturing in presence of NO3-N alone or combination with NH4-N up to equimolar concentrations resulted in complete nitrogen uptake, increased growth in both the microbial strains, and enhanced accumulation of carbohydrates, proteins, and lipids. Total chlorophyll content in microalga was also significantly higher when it was grown as a co-culture with NO3-N and NH4-N up to a ratio of 50:50. Significant upregulation in the synthesis of amino acids and sugars and downregulation of organic acids were evident with higher ammonium uptake in the co-culture, indicating the regulation of carbon and nitrogen assimilation pathways and energy synthesis. Our data suggest that the co-culture of strains IS1 and IS2 could be exploited for effluent treatment by considering the concentrations of inorganic sources, particularly ammonium, in the wastewaters.
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Affiliation(s)
- Isiri Adhiwarie Perera
- Global Centre for, Environmental Remediation (GCER), School of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, NSW, 2308, Callaghan, Australia
| | - Sudharsanam Abinandan
- Global Centre for, Environmental Remediation (GCER), School of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, NSW, 2308, Callaghan, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Suresh R Subashchandrabose
- Global Centre for, Environmental Remediation (GCER), School of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, NSW, 2308, Callaghan, Australia
| | - Kadiyala Venkateswarlu
- Formerly Department of Microbiology, Sri Krishnadevaraya University, Anantapuramu, 515003, Andhra Pradesh, India
| | - Ravi Naidu
- Global Centre for, Environmental Remediation (GCER), School of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, NSW, 2308, Callaghan, Australia
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia
| | - Mallavarapu Megharaj
- Global Centre for, Environmental Remediation (GCER), School of Engineering, Science and Environment, The University of Newcastle, ATC Building, University Drive, NSW, 2308, Callaghan, Australia.
- Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE), The University of Newcastle, ATC Building, University Drive, Callaghan, NSW, 2308, Australia.
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Kamikawa R, Mochizuki T, Sakamoto M, Tanizawa Y, Nakayama T, Onuma R, Cenci U, Moog D, Speak S, Sarkozi K, Toseland A, van Oosterhout C, Oyama K, Kato M, Kume K, Kayama M, Azuma T, Ishii KI, Miyashita H, Henrissat B, Lombard V, Win J, Kamoun S, Kashiyama Y, Mayama S, Miyagishima SY, Tanifuji G, Mock T, Nakamura Y. Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. SCIENCE ADVANCES 2022; 8:eabi5075. [PMID: 35486731 PMCID: PMC9054022 DOI: 10.1126/sciadv.abi5075] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.
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Affiliation(s)
- Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takako Mochizuki
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Mika Sakamoto
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
| | - Takuro Nakayama
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Ugo Cenci
- Université de Lille, CNRS, UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8
- SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Samuel Speak
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Krisztina Sarkozi
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrew Toseland
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Kaori Oyama
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Keitaro Kume
- Department of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonori Azuma
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Ken-ichiro Ishii
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yuichiro Kashiyama
- Graduate School of Engineering, Fukui University of Technology, Fukui, Japan
| | - Shigeki Mayama
- Advanced Support Center for Science Teachers, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Goro Tanifuji
- Department of Zoology, National Museum of Nature and Science, Tsukuba 305-0005, Japan
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Research Organization of Information and Systems, Shizuoka 411-8540, Japan
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36
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Régimbeau A, Budinich M, Larhlimi A, Pierella Karlusich JJ, Aumont O, Memery L, Bowler C, Eveillard D. Contribution of genome-scale metabolic modelling to niche theory. Ecol Lett 2022; 25:1352-1364. [PMID: 35384214 PMCID: PMC9324083 DOI: 10.1111/ele.13954] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/22/2021] [Accepted: 11/28/2021] [Indexed: 12/22/2022]
Abstract
Standard niche modelling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome‐scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that resumes the whole metabolic capabilities of an organism. The so‐called metabolic niche resumes well‐known traits such as nutrient needs and their dependencies for survival. Despite the computational challenge, its implementation allows the detection of traits and the formal comparison of niches of different organisms, emphasising that the presence–absence of functional genes is not enough to approximate the phenotype. Further statistical exploration of an organism's niche sheds light on genes essential for the metabolic niche and their role in understanding various biological experiments, such as transcriptomics, paving the way for incorporating better genome‐scale description in ecological studies.
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Affiliation(s)
| | | | | | - Juan José Pierella Karlusich
- Département de Biologie, Institut de Biologie de l'ENS, École Normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Olivier Aumont
- Laboratoire d'Océanographie et du Climat: Expérimentations et Approches Numériques (LOCEAN), IRD-IPSL, Paris, France
| | - Laurent Memery
- Université de Brest (UBO), CNRS, IRD, Ifremer, Laboratoire des Sciences de l'Environnement Marin, Plouzané, France
| | - Chris Bowler
- Département de Biologie, Institut de Biologie de l'ENS, École Normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GO-SEE, Paris, France
| | - Damien Eveillard
- Université de Nantes, CNRS, LS2N, Nantes, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GO-SEE, Paris, France
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Optimal Nitrate Supplementation in Phaeodactylum tricornutum Culture Medium Increases Biomass and Fucoxanthin Production. Foods 2022; 11:foods11040568. [PMID: 35206051 PMCID: PMC8871257 DOI: 10.3390/foods11040568] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 12/31/2022] Open
Abstract
Phaeodactylum tricornutum is a model diatom with numerous potential applications in the industry, including the production of high-value carotenoid pigments such as fucoxanthin. This compound is a potent antioxidant currently extracted mainly from brown macroalgae. Fucoxanthin exhibits several biological properties with well-known beneficial effects in the treatment and prevention of lifestyle-related diseases. P. tricornutum offers a valuable alternative to macroalgae for fucoxanthin production as it has a specific productivity that is 10-fold higher as compared with macroalgae. However, production processes still need to be optimised to become a cost-effective alternative. In this work, we investigated the optimal supplementation of nitrate in a cultivation medium that is currently used for P. tricornutum and how this nitrate concentration affects cell growth and fucoxanthin production. It has previously been shown that the addition of sodium nitrate increases productivity, but optimal conditions were not accurately determined. In this report, we observed that the continuous increase in nitrate concentration did not lead to an increase in biomass and fucoxanthin content, but there was rather a window of optimal values of nitrate that led to maximum growth and pigment production. These results are discussed considering both the scale up for industrial production and the profitability of the process, as well as the implications in the cell’s metabolism and effects in fucoxanthin production.
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38
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Xie X, Du H, Chen J, Aslam M, Wang W, Chen W, Li P, Du H, Liu X. Global Profiling of N-Glycoproteins and N-Glycans in the Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2021; 12:779307. [PMID: 34925422 PMCID: PMC8678454 DOI: 10.3389/fpls.2021.779307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/05/2021] [Indexed: 05/04/2023]
Abstract
N-glycosylation is an important posttranslational modification in all eukaryotes, but little is known about the N-glycoproteins and N-glycans in microalgae. Here, N-glycoproteomic and N-glycomic approaches were used to unveil the N-glycoproteins and N-glycans in the model diatom Phaeodactylum tricornutum. In total, 863 different N-glycopeptides corresponding to 639 N-glycoproteins were identified from P. tricornutum. These N-glycoproteins participated in a variety of important metabolic pathways in P. tricornutum. Twelve proteins participating in the N-glycosylation pathway were identified as N-glycoproteins, indicating that the N-glycosylation of these proteins might be important for the protein N-glycosylation pathway. Subsequently, 69 N-glycans corresponding to 59 N-glycoproteins were identified and classified into high mannose and hybrid type N-glycans. High mannose type N-glycans contained four different classes, such as Man-5, Man-7, Man-9, and Man-10 with a terminal glucose residue. Hybrid type N-glycan harbored Man-4 with a terminal GlcNAc residue. The identification of N-glycosylation on nascent proteins expanded our understanding of this modification at a N-glycoproteomic scale, the analysis of N-glycan structures updated the N-glycan database in microalgae. The results obtained from this study facilitate the elucidation of the precise function of these N-glycoproteins and are beneficial for future designing the microalga to produce the functional humanized biopharmaceutical N-glycoproteins for the clinical therapeutics.
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Affiliation(s)
- Xihui Xie
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Jichen Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Muhammad Aslam
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Faculty of Marine Sciences, Lasbela University of Agriculture, Water & Marine Sciences, Uthal, Pakistan
| | - Wanna Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Weizhou Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Ping Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
| | - Hua Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, College of Sciences, Institute of Marine Sciences, Shantou University, Shantou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
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39
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Wei L, You W, Xu Z, Zhang W. Transcriptomic survey reveals multiple adaptation mechanisms in response to nitrogen deprivation in marine Porphyridium cruentum. PLoS One 2021; 16:e0259833. [PMID: 34793503 PMCID: PMC8601545 DOI: 10.1371/journal.pone.0259833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 09/28/2021] [Indexed: 11/19/2022] Open
Abstract
Single-cell red microalga Porphyridium cruentum is potentially considered to be the bioresource for biofuel and pharmaceutical production. Nitrogen is a kind of nutrient component for photosynthetic P. cruentum. Meanwhile, nitrogen stress could induce to accumulate some substances such as lipid and phycoerythrin and affect its growth and physiology. However, how marine microalga Porphyridium cruentum respond and adapt to nitrogen starvation remains elusive. Here, acclimation of the metabolic reprogramming to changes in the nutrient environment was studied by high-throughput mRNA sequencing in the unicellular red alga P. cruentum. Firstly, to reveal transcriptional regulation, de novo transcriptome was assembled and 8,244 unigenes were annotated based on different database. Secondly, under nitrogen deprivation, 2100 unigenes displayed differential expression (1134 upregulation and 966 downregulation, respectively) and some pathways including carbon/nitrogen metabolism, photosynthesis, and lipid metabolism would be reprogrammed in P. cruentum. The result demonstrated that nitrate assimilation (with related unigenes of 8–493 fold upregulation) would be strengthen and photosynthesis (with related unigenes of 6–35 fold downregulation) be impaired under nitrogen deprivation. Importantly, compared to other green algae, red microalga P. cruentum presented a different expression pattern of lipid metabolism in response to nitrogen stress. These observations will also provide novel insight for understanding adaption mechanisms and potential targets for metabolic engineering and synthetic biology in P. cruentum.
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Affiliation(s)
- Li Wei
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- * E-mail: (LW); (WZ)
| | - Wuxin You
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Zhengru Xu
- College of Foreign Language, Hainan Normal University, Haikou, China
| | - Wenfei Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
- * E-mail: (LW); (WZ)
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40
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Phytate as a phosphorus nutrient with impacts on iron stress-related gene expression for phytoplankton: insights from diatom Phaeodactylum tricornutum. Appl Environ Microbiol 2021; 88:e0209721. [PMID: 34757820 DOI: 10.1128/aem.02097-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phytoplankton have evolved a capability to acquire phosphorus (P) from dissolved organic phosphorus (DOP) since the preferred form, dissolved inorganic phosphate (DIP, or Pi), is often limited in parts of the ocean. Phytic acid (PA) is abundantly synthesized in plants and rich in excreta of animals, potentially enriching the DOP pool in coastal oceans. However, whether and how PA may be used by phytoplankton are poorly understood. Here, we investigated PA utilization and underlying metabolic pathways in the diatom model Phaeodactylum tricornutum. The physiological results showed that P. tricornutum could utilize PA as a sole source of P nutrient to support growth. Meanwhile, the replacement of PA for DIP also caused changes in multiple cellular processes such as inositol phosphate metabolism, photosynthesis, and signal transduction. These results suggest that PA is bioavailable to P. tricornutum and can directly participate the metabolic pathways of PA-grown cells. However, our data showed that the utilization of PA was markedly less efficient than that of DIP, and PA-grown cells exhibited P and iron (Fe) nutrient stress signals. Implicated in these findings is the potential of complicated responses of phytoplankton to an ambient DOP species, which calls for more systematic investigation. IMPORTANCE PA is abundant in plants, and cannot be digested by non-ruminant animals. Hence, it is potentially a significant component of the DOP pool in the coastal waters. Despite the potential importance, there is little information about its bioavailability to phytoplankton as a source of P nutrient and if so what molecular mechanisms are involved. In this study, we found that part of PA could be utilized by the diatom P. tricornutum to support growth, and another portion of PA can act as a substrate directly participating in various metabolism pathways and cellular processes. However, our physiological and transcriptomic data show that PA-grown cells still exhibited signs of P stress and potential Fe stress. These results have significant implications in phytoplankton P nutrient ecology and provide a novel insight into multi-faceted impacts of DOP utilization on phytoplankton nutrition and metabolism.
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Bi R, Cao Z, Ismar-Rebitz SMH, Sommer U, Zhang H, Ding Y, Zhao M. Responses of Marine Diatom-Dinoflagellate Competition to Multiple Environmental Drivers: Abundance, Elemental, and Biochemical Aspects. Front Microbiol 2021; 12:731786. [PMID: 34526982 PMCID: PMC8435848 DOI: 10.3389/fmicb.2021.731786] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Ocean-related global change has strongly affected the competition between key marine phytoplankton groups, such as diatoms and dinoflagellates, especially with the deleterious consequency of the increasing occurrence of harmful algal blooms. The dominance of diatoms generally shifts toward that of dinoflagellates in response to increasing temperature and reduced nutrient availability; however, contradictory findings have also been observed in certain sea areas. A key challenge in ecology and biogeochemistry is to quantitatively determine the effects of multiple environmental factors on the diatom-dinoflagellate community and the related changes in elemental and biochemical composition. Here, we test the interplay between temperature, nutrient concentrations and their ratios on marine diatom-dinoflagellate competition and chemical composition using bi-algal competition experiments. The ubiquitous diatom Phaeodactylum tricornutum and dinoflagellate Prorocentrum minimum were cultivated semi-continuously, provided with different N and P concentrations (three different levels) and ratios (10:1, 24:1, and 63:1 molar ratios) under three temperatures (12, 18, and 24°C). The responses of diatom-dinoflagellate competition were analyzed by a Lotka-Volterra model and quantified by generalized linear mixed models (GLMMs) and generalized additive models (GAMs). The changes in nutrient concentrations significantly affected diatom-dinoflagellate competition, causing a competitive superiority of the diatoms at high nutrient concentrations, independent of temperature and N:P supply ratios. Interestingly, the effect amplitude of nutrient concentrations varied with different temperatures, showing a switch back toward a competitive superiority of the dinoflagellates at the highest temperature and at very high nutrient concentrations. The ratios of particulate organic nitrogen to phosphorus showed significant negative correlations with increasing diatoms/dinoflagellates ratios, while lipid biomarkers (fatty acids and sterols) correlated positively with increasing diatoms/dinoflagellates ratios over the entire ranges of temperature, N and P concentrations and N:P ratios. Our results indicate that the integration of phytoplankton community structure and chemical composition provides an important step forward to quantitatively understand and predict how phytoplankton community changes affect ecosystem functions and biogeochemical cycles in the ocean.
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Affiliation(s)
- Rong Bi
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, Ministry of Education, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Zhong Cao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, Ministry of Education, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | | | - Ulrich Sommer
- Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Hailong Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, Ministry of Education, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yang Ding
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, Ministry of Education, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Meixun Zhao
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and Key Laboratory of Marine Chemistry Theory and Technology, Ocean University of China, Ministry of Education, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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42
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Rodriguez-Rivera FP, Levi SM. Unifying Catalysis Framework to Dissect Proteasomal Degradation Paradigms. ACS CENTRAL SCIENCE 2021; 7:1117-1125. [PMID: 34345664 PMCID: PMC8323112 DOI: 10.1021/acscentsci.1c00389] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Indexed: 06/13/2023]
Abstract
Diverging from traditional target inhibition, proteasomal protein degradation approaches have emerged as novel therapeutic modalities that embody distinct pharmacological profiles and can access previously undrugged targets. Small molecule degraders have the potential to catalytically destroy target proteins at substoichiometric concentrations, thus lowering administered doses and extending pharmacological effects. With this mechanistic premise, research efforts have advanced the development of small molecule degraders that benefit from stable and increased affinity ternary complexes. However, a holistic framework that evaluates different degradation modes from a catalytic perspective, including focusing on kinetically favored degradation mechanisms, is lacking. In this Outlook, we introduce the concept of an induced cooperativity spectrum as a unifying framework to mechanistically understand catalytic degradation profiles. This framework is bolstered by key examples of published molecular degraders extending from molecular glues to bivalent degraders. Critically, we discuss remaining challenges and future opportunities in drug discovery to rationally design and phenotypically screen for efficient degraders.
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Affiliation(s)
- Frances P. Rodriguez-Rivera
- Discovery
Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Samuel M. Levi
- Pfizer
Worldwide Research and Development, Pfizer,
Inc., 1 Portland Street, Cambridge, Massachusetts 02139, United States
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43
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Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean. Proc Natl Acad Sci U S A 2021; 118:2107238118. [PMID: 34301906 PMCID: PMC8325266 DOI: 10.1073/pnas.2107238118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Phytoplankton contribute to the Southern Ocean’s (SO) ability to absorb atmospheric CO2 and shape the stoichiometry of northward macronutrient delivery. Climate change is altering the SO environment, yet we know little about how resident phytoplankton will react to these changes. Here, we studied a natural SO community and compared responses of two prevalent, bloom-forming diatom groups to changes in temperature and iron that are projected to occur by 2100 to 2300. We found that one group, Pseudo-nitzschia, grows better under warmer low-iron conditions by managing cellular iron demand and efficiently increasing photosynthetic capacity. This ability to grow and draw down nutrients in the face of warming, regardless of iron availability, has major implications for ocean ecosystems and global nutrient cycles. The Southern Ocean (SO) harbors some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how these changes will influence community composition and downstream biogeochemical processes. We performed light-saturated experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea to examine the effects of increased iron availability (+2 nM) and warming (+3 and +6 °C) on nutrient uptake, as well as the growth and transcriptional responses of two dominant diatoms, Fragilariopsis and Pseudo-nitzschia. We found that community nutrient uptake and primary productivity were elevated under both warming conditions without iron addition (relative to ambient −0.5 °C). This effect was greater than additive under concurrent iron addition and warming. Pseudo-nitzschia became more abundant under warming without added iron (especially at 6 °C), while Fragilariopsis only became more abundant under warming in the iron-added treatments. We attribute the apparent advantage Pseudo-nitzschia shows under warming to up-regulation of iron-conserving photosynthetic processes, utilization of iron-economic nitrogen assimilation mechanisms, and increased iron uptake and storage. These data identify important molecular and physiological differences between dominant diatom groups and add to the growing body of evidence for Pseudo-nitzschia’s increasingly important role in warming SO ecosystems. This study also suggests that temperature-driven shifts in SO phytoplankton assemblages may increase utilization of the vast pool of excess nutrients in iron-limited SO surface waters and thereby influence global nutrient distribution and carbon cycling.
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44
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Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes. Proc Natl Acad Sci U S A 2021; 118:2009974118. [PMID: 33419955 DOI: 10.1073/pnas.2009974118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.
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45
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Gomaa F, Utter DR, Powers C, Beaudoin DJ, Edgcomb VP, Filipsson HL, Hansel CM, Wankel SD, Zhang Y, Bernhard JM. Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. SCIENCE ADVANCES 2021; 7:7/22/eabf1586. [PMID: 34039603 PMCID: PMC8153729 DOI: 10.1126/sciadv.abf1586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/05/2021] [Indexed: 05/14/2023]
Abstract
Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.
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Affiliation(s)
- Fatma Gomaa
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Powers
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - David J Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Joan M Bernhard
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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46
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Santin A, Caputi L, Longo A, Chiurazzi M, Ribera d'Alcalà M, Russo MT, Ferrante MI, Rogato A. Integrative omics identification, evolutionary and structural analysis of low affinity nitrate transporters in diatoms, diNPFs. Open Biol 2021; 11:200395. [PMID: 33823659 PMCID: PMC8025304 DOI: 10.1098/rsob.200395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diatoms are one of the major and most diverse groups of phytoplankton, with chimeric genomes harbouring a combination of genes of bacterial, animal and plant origin. They have developed sophisticated mechanisms to face environmental variations. In marine environments, nutrients concentration shows significant temporal and spatial variability, influencing phytoplankton growth. Among nutrients, nitrogen, present at micromolar levels, is often a limiting resource. Here, we report a comprehensive characterization of the Nitrate Transporter 1/Peptide Transporter Family (NPF) in diatoms, diNPFs. NPFs are well characterized in many organisms where they recognize a broad range of substrates, ranging from short-chained di- and tri-peptides in bacteria, fungi and mammals to a wide variety of molecules including nitrate in higher plants. Scarce information is available for diNPFs. We integrated-omics, phylogenetic, structural and expression analyses, to infer information on their role in diatoms. diNPF genes diverged to produce two distinct clades with strong sequence and structural homology with either bacterial or plant NPFs, with different predicted sub-cellular localization, suggesting that the divergence resulted in functional diversification. Moreover, transcription analysis of diNPF genes under different laboratory and environmental growth conditions suggests that diNPF diversification led to genetic adaptations that might contribute to diatoms ability to flourish in diverse environmental conditions.
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Affiliation(s)
- Anna Santin
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Luigi Caputi
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Antonella Longo
- BioDiscovery Institute, Denton, TX, USA.,Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | | | | | | | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.,Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
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Representative Diatom and Coccolithophore Species Exhibit Divergent Responses throughout Simulated Upwelling Cycles. mSystems 2021; 6:6/2/e00188-21. [PMID: 33785571 PMCID: PMC8546972 DOI: 10.1128/msystems.00188-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Wind-driven upwelling followed by relaxation results in cycles of cold nutrient-rich water fueling intense phytoplankton blooms followed by nutrient depletion, bloom decline, and sinking of cells. Surviving cells at depth can then be vertically transported back to the surface with upwelled waters to seed another bloom. As a result of these cycles, phytoplankton communities in upwelling regions are transported through a wide range of light and nutrient conditions. Diatoms appear to be well suited for these cycles, but their responses to them remain understudied. To investigate the bases for diatoms’ ecological success in upwelling environments, we employed laboratory simulations of a complete upwelling cycle with a common diatom, Chaetoceros decipiens, and coccolithophore, Emiliania huxleyi. We show that while both organisms exhibited physiological and transcriptomic plasticity, the diatom displayed a distinct response enabling it to rapidly shift-up growth rates and nitrate assimilation when returned to light and available nutrients following dark nutrient-deplete conditions. As observed in natural diatom communities, C. decipiens highly expresses before upwelling, or frontloads, key transcriptional and nitrate assimilation genes, coordinating its rapid response to upwelling conditions. Low-iron simulations showed that C. decipiens is capable of maintaining this response when iron is limiting to growth, whereas E. huxleyi is not. Differential expression between iron treatments further revealed specific genes used by each organism under low iron availability. Overall, these results highlight the responses of two dominant phytoplankton groups to upwelling cycles, providing insight into the mechanisms fueling diatom blooms during upwelling events. IMPORTANCE Coastal upwelling regions are among the most biologically productive ecosystems. During upwelling events, nutrient-rich water is delivered from depth resulting in intense phytoplankton blooms typically dominated by diatoms. Along with nutrients, phytoplankton may also be transported from depth to seed these blooms then return to depth as upwelling subsides creating a cycle with varied conditions. To investigate diatoms’ success in upwelling regions, we compare the responses of a common diatom and coccolithophore throughout simulated upwelling cycles under iron-replete and iron-limiting conditions. The diatom exhibited a distinct rapid response to upwelling irrespective of iron status, whereas the coccolithophore’s response was either delayed or suppressed depending on iron availability. Concurrently, the diatom highly expresses, or frontloads, nitrate assimilation genes prior to upwelling, potentially enabling this rapid response. These results provide insight into the molecular mechanisms underlying diatom blooms and ecological success in upwelling regions.
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48
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Thamatrakoln K. Diatom Ecophysiology: Crossing Signals on the Road to Recovery from Nutrient Deprivation. Curr Biol 2021; 31:R253-R254. [PMID: 33689725 DOI: 10.1016/j.cub.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A new study reveals that phosphorus-limited diatoms employ a rapid calcium-based signaling pathway upon phosphorus resupply. This response leads to enhanced nitrogen uptake and assimilation, setting the stage for recovery from nutrient deprivation.
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Affiliation(s)
- Kimberlee Thamatrakoln
- Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
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49
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Helliwell KE, Harrison EL, Christie-Oleza JA, Rees AP, Kleiner FH, Gaikwad T, Downe J, Aguilo-Ferretjans MM, Al-Moosawi L, Brownlee C, Wheeler GL. A Novel Ca 2+ Signaling Pathway Coordinates Environmental Phosphorus Sensing and Nitrogen Metabolism in Marine Diatoms. Curr Biol 2020; 31:978-989.e4. [PMID: 33373640 DOI: 10.1016/j.cub.2020.11.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/26/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
Diatoms are a diverse and globally important phytoplankton group, responsible for an estimated 20% of carbon fixation on Earth. They frequently form spatially extensive phytoplankton blooms, responding rapidly to increased availability of nutrients, including phosphorus (P) and nitrogen (N). Although it is well established that diatoms are common first responders to nutrient influxes in aquatic ecosystems, little is known of the sensory mechanisms that they employ for nutrient perception. Here, we show that P-limited diatoms use a Ca2+-dependent signaling pathway, not previously described in eukaryotes, to sense and respond to the critical macronutrient P. We demonstrate that P-Ca2+ signaling is conserved between a representative pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom. Moreover, this pathway is ecologically relevant, being sensitive to sub-micromolar concentrations of inorganic phosphate and a range of environmentally abundant P forms. Notably, we show that diatom recovery from P limitation requires rapid and substantial increases in N assimilation and demonstrate that this process is dependent on P-Ca2+ signaling. P-Ca2+ signaling thus governs the capacity of diatoms to rapidly sense and respond to P resupply, mediating fundamental cross-talk between the vital nutrients P and N and maximizing diatom resource competition in regions of pulsed nutrient supply.
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Affiliation(s)
- Katherine E Helliwell
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
| | - Ellen L Harrison
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | - Andrew P Rees
- Plymouth Marine Laboratory, Plymouth, Devon PL1 3DH, UK
| | - Friedrich H Kleiner
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Trupti Gaikwad
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Joshua Downe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | | | - Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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50
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Mann M, Serif M, Wrobel T, Eisenhut M, Madhuri S, Flachbart S, Weber APM, Lepetit B, Wilhelm C, Kroth PG. The Aureochrome Photoreceptor PtAUREO1a Is a Highly Effective Blue Light Switch in Diatoms. iScience 2020; 23:101730. [PMID: 33235981 PMCID: PMC7670200 DOI: 10.1016/j.isci.2020.101730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/30/2020] [Accepted: 10/21/2020] [Indexed: 02/08/2023] Open
Abstract
Aureochromes represent a unique type of blue light photoreceptors that possess a blue light sensing flavin-binding LOV-domain and a DNA-binding bZIP domain, thus being light-driven transcription factors. The diatom Phaeodactylum tricornutum, a member of the essential marine primary producers, possesses four aureochromes (PtAUREO1a, 1b, 1c, 2). Here we show a dramatic change in the global gene expression pattern of P. tricornutum wild-type cells after a shift from red to blue light. About 75% of the genes show significantly changed transcript levels already after 10 and 60 min of blue light exposure, which includes genes of major transcription factors as well as other photoreceptors. Very surprisingly, this light-induced regulation of gene expression is almost completely inhibited in independent PtAureo1a knockout lines. Such a massive and fast transcriptional change depending on one single photoreceptor is so far unprecedented. We conclude that PtAUREO1a plays a key role in diatoms upon blue light exposure. Blue light induces a very fast transcriptional response in the diatom P. tricornutum This strong response is almost completely inhibited when Aureochrome 1a is absent The results imply a key role of PtAureo1a in blue light-induced responses in diatoms
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Affiliation(s)
- Marcus Mann
- Institut für Biologie, Universität Leipzig, 04009 Leipzig, Germany
| | - Manuel Serif
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Thomas Wrobel
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Marion Eisenhut
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Shvaita Madhuri
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Samantha Flachbart
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Bernard Lepetit
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | | | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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