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Li H, Chen J, Yu L, Fan G, Li T, Li L, Yuan H, Wang J, Wang C, Li D, Lin S. In situ community transcriptomics illuminates CO 2-fixation potentials and supporting roles of phagotrophy and proton pump in plankton in a subtropical marginal sea. Microbiol Spectr 2024; 12:e0217723. [PMID: 38319114 PMCID: PMC10913738 DOI: 10.1128/spectrum.02177-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Lineage-wise physiological activities of plankton communities in the ocean are important but challenging to characterize. Here, we conducted whole-assemblage metatranscriptomic profiling at continental shelf and slope sites in the South China Sea to investigate carbon fixation potential in different lineages. RuBisCO expression, the proxy of Calvin carbon fixation (CCF) potential, was mainly contributed by Bacillariophyta, Chlorophyta, Cyanobacteria, and Haptophyta, which was differentially affected by environmental factors among lineages. CCF potential exhibited positive or negative correlations with phagotrophy gene expression, suggesting phagotrophy possibly enhances or complements CCF. Our data also reveal significant non-Calvin carbon fixation (NCF) potential, as indicated by the active expression of genes in all five currently recognized NCF pathways, mainly contributed by Flavobacteriales, Alteromonadales, and Oceanospirillales. Furthermore, in Flavobacteriales, Alteromonadales, Pelagibacterales, and Rhodobacterales, NCF potential was positively correlated with proton-pump rhodopsin (PPR) expression, suggesting that NCF might be energetically supported by PPR. The novel insights into the lineage-differential potential of carbon fixation, widespread mixotrophy, and PPR as an energy source for NCF lay a methodological and informational foundation for further research to understand carbon fixation and the trophic landscape in the ocean.IMPORTANCEMarine plankton plays an important role in global carbon cycling and climate regulation. Phytoplankton and cyanobacteria fix CO2 to produce organic compounds using solar energy and mainly by the Calvin cycle, whereas autotrophic bacteria and archaea may fix CO2 by non-Calvin cycle carbon fixation pathways. How active individual lineages are in carbon fixation and mixotrophy, and what energy source bacteria may employ in non-Calvin carbon fixation, in a natural plankton assemblage are poorly understood and underexplored. Using metatranscriptomics, we studied carbon fixation in marine plankton with lineage resolution in tropical marginal shelf and slope areas. Based on the sequencing results, we characterized the carbon fixation potential of different lineages and assessed Calvin- and non-Calvin- carbon fixation activities and energy sources. Data revealed a high number of unigenes (4.4 million), lineage-dependent differential potentials of Calvin carbon fixation and responses to environmental conditions, major contributors of non-Calvin carbon fixation, and their potential energy source.
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Affiliation(s)
- Hongfei Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, Zhejiang, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
| | - Jianwei Chen
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Guangyi Fan
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, Guangdong, China
| | - Tangcheng Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Huatao Yuan
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Jingtian Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Denghui Li
- Qingdao Key Laboratory of Marine Genomics, BGI Research, Qingdao, Shandong, China
- Qingdao Innovation Center of Seaweed Biotechnology, Qingdao, Shandong, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, USA
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Chen H, Hu Y, Yang G, Li P, Yin J, Feng X, Wu Q, Zhang J, Xiao B, Sui Z. Macropinocytosis in Gracilariopsis lemaneiformis (Rhodophyta). FRONTIERS IN PLANT SCIENCE 2023; 14:1225675. [PMID: 37822336 PMCID: PMC10562585 DOI: 10.3389/fpls.2023.1225675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023]
Abstract
Macropinocytosis is an endocytic process that plays an important role in animal development and disease occurrence but until now has been rarely reported in organisms with cell walls. We investigated the properties of endocytosis in a red alga, Gracilariopsis lemaneiformis. The cells non-selectively internalized extracellular fluid into large-scale endocytic vesicles (1.94 ± 0.51 μm), and this process could be inhibited by 5-(N-ethyl-N-isopropyl) amiloride, an macropinocytosis inhibitor. Moreover, endocytosis was driven by F-actin, which promotes formation of ruffles and cups from the cell surface and facilitates formation of endocytotic vesicles. After vesicle formation, endocytic vesicles could be acidified and acquire digestive function. These results indicated macropinocytosis in G. lemaneiformis. Abundant phosphatidylinositol kinase and small GTPase encoding genes were found in the genome of this alga, while PI3K, Ras, and Rab5, the important participators of traditional macropinocytosis, seem to be lacked. Such findings provide a new insight into endocytosis in organisms with cell walls and facilitate further research into the core regulatory mechanisms and evolution of macropinocytosis.
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Affiliation(s)
- Haihong Chen
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang, China
| | - Yiyi Hu
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Guanpin Yang
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
- Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Pingping Li
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Jingru Yin
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Xiaoqing Feng
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Qiong Wu
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Jingyu Zhang
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Baoheng Xiao
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, China
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Transcriptomic-Guided Phosphonate Utilization Analysis Unveils Evidence of Clathrin-Mediated Endocytosis and Phospholipid Synthesis in the Model Diatom, Phaeodactylum tricornutum. mSystems 2022; 7:e0056322. [PMID: 36317887 PMCID: PMC9765203 DOI: 10.1128/msystems.00563-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Phosphonates are important components of marine organic phosphorus, but their bioavailability and catabolism by eukaryotic phytoplankton remain enigmatic. Here, diatom Phaeodactylum tricornutum was used to investigate the bioavailability of phosphonates and describe the underlying molecular mechanism. The results showed that 2-aminoethylphosphonic acid (2-AEP) can be utilized as an alternative phosphorus source. Comparative transcriptomics revealed that the utilization of 2-AEP comprised 2 steps, including molecular uptake through clathrin-mediated endocytosis and incorporation into the membrane phospholipids in the form of diacylglyceryl-2-AEP (DAG-2-AEP). In the global ocean, we found the prevalence and dynamic expression pattern of key genes that are responsible for vesicle formation (CLTC, AP-2) and DAG-AEP synthesis (PCYT2, EPT1) in diatom assemblages. This study elucidates a distinctive mechanism of phosphonate utilization by diatoms, and discusses the ecological implications. IMPORTANCE Phosphonates contribute ~25% of total dissolved organic phosphorus in the ocean, and are found to be important for marine phosphorus biogeochemical cycle. As a type of biogenic phosphonate produced by microorganisms, 2-aminoethylphosphonic acid (2-AEP) widely exists in the ocean. It is well known that 2-AEP can be cleaved and utilized by prokaryotes, but its ability to support the growth of eukaryotic phytoplankton remains unclear. Our research identified the bioavailability of 2-AEP for the diatom Phaeodactylum tricornutum, and proposed a distinctive metabolic pathway of 2-AEP utilization. Different from the enzymatic hydrolysis of phosphonates, the results suggested that P. tricornutum utilizes 2-AEP by incorporating it into phospholipid instead of cleaving the C-P bond. Moreover, the ubiquitous distribution of associated representative gene transcripts in the environmental assemblages and the higher gene transcript abundance in the cold regions were observed, which suggests the possible environmental adaption of 2-AEP utilization by diatoms.
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Mehmood S, Mahmood M, Núñez-Delgado A, Alatalo JM, Elrys AS, Rizwan M, Weng J, Li W, Ahmed W. A green method for removing chromium (VI) from aqueous systems using novel silicon nanoparticles: Adsorption and interaction mechanisms. ENVIRONMENTAL RESEARCH 2022; 213:113614. [PMID: 35710023 DOI: 10.1016/j.envres.2022.113614] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/24/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
In the present study, we used the horsetail plant (Equisetum arvense) as a green source to synthesize silicon nanoparticles (GS-SiNPs), considering that it could be an effective adsorbent for removing chromium (Cr (VI)) from aqueous solutions. The characterization of GS-SiNPs was performed via Brunauer-Emmett-Teller (BET), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and X-ray photo electron spectroscopy (XPS) techniques. The batch test results of Cr (VI) adsorption on GS-SiNPs showed a high adsorption capacity, reaching 87.9% of the amount added. The pseudo-second order kinetic model was able to comprehensively explain the adsorption kinetics and provided a maximum Cr (VI) adsorption capacity (Qe) of 3.28 mg g-1 (R2 = 90.68), indicating fast initial adsorption by the diffusion process. The Langmuir isotherm model fitted the experimental data, and accurately simulated the adsorption of Cr (VI) on GS-SiNPs (R2 = 97.79). FTIR and XPS spectroscopy gave further confirmation that the main mechanism was ion exchange with Cr and surface complexation through -OH and -COOH. Overall, the results of the research can be of relevance as regards a green and new alternative for the removal of Cr (VI) pollution from affected environments.
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Affiliation(s)
- Sajid Mehmood
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, 570100, China; College of Ecology and Environment, Hainan University, Haikou City, 570100, China
| | - Mohsin Mahmood
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, 570100, China; College of Ecology and Environment, Hainan University, Haikou City, 570100, China
| | - Avelino Núñez-Delgado
- Department of Soil Science and Agricultural Chemistry, Engineering Polytechnic School, University of Santiago de Compostela, Campus Univ. s/n, 27002, Lugo, Univ. Santiago de Compostela, Spain
| | - Juha M Alatalo
- Environmental Science Center, Qatar University, Doha, Qatar
| | - Ahmed S Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Muhammad Rizwan
- Agricultural Research Station, Office of VP for Research & Graduate Studies, Qatar University, 2713, Doha, Qatar
| | - Jiechang Weng
- Hainan Provincial Ecological and Environmental Monitoring Center, 571126, China
| | - Weidong Li
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, 570100, China; College of Ecology and Environment, Hainan University, Haikou City, 570100, China.
| | - Waqas Ahmed
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, Hainan University, Haikou, 570100, China; College of Ecology and Environment, Hainan University, Haikou City, 570100, China.
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Reid A, Buchanan F, Julius M, Walsh PJ. A review on diatom biosilicification and their adaptive ability to uptake other metals into their frustules for potential application in bone repair. J Mater Chem B 2021; 9:6728-6737. [PMID: 34346480 DOI: 10.1039/d1tb00322d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diatoms are unicellular eukaryotic algae that have a distinctive siliceous cell wall (frustule) with unique architectures. The nanotopography of the frustule is perfectly replicated between generations, offering a source of highly intricate and identical silica microparticles. In recent years, the ability to alter their cell wall chemistry both in terms of functionalisation with organic moieties or by incorporation of the metal ions in their frustules has increased interest in their utility for catalysis technologies, and semiconductor and biomedical applications. Herein we review the fundamental biological mechanisms in which diatoms produce their frustule and their ability to substitute different metal ions in their frustule fabrication process. The review focuses on the potential of diatom frustules as a naturally derived biomaterial in bone tissue engineering applications and how their cell walls, comprising biogenic silica, could either partially or fully incorporate other bone therapeutic metal ions, e.g., titanium or calcium, into their frustule. The use of diatom frustules in bone repair also potentially offers a 'greener', more environmentally friendly, biomaterial as they can naturally synthesise oxides of silicon and other metals into their frustules under ambient conditions at a relatively neutral pH. This process would negate the use of harsh organic chemicals and high-temperature processing conditions, often used in the fabrication of silica based biomaterials, e.g., bioactive glass.
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Affiliation(s)
- A Reid
- School of Chemistry & Chemical Engineering, Queen's University, Belfast, UK.
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