1
|
Shi J, Hu M, Xia Z, Zhang J, Wang Z, Li L, Zhao Y. Influence of perfluoroalkyl substances, with focus on perfluorobutanoic acid on the responding characteristics and molecular mechanisms of Thalassiosira pseudonana. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 285:117048. [PMID: 39288731 DOI: 10.1016/j.ecoenv.2024.117048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 09/08/2024] [Accepted: 09/12/2024] [Indexed: 09/19/2024]
Abstract
Perfluoroalkyl substances (PFAS) are widely dispersed persistent organic pollutants (POPs) throughout marine ecosystems. Due to ban of traditional long-chain PFAS, the emerging short-chain ones showed increased environmental detection as substitutes. As the foundation of aquatic food webs, microalgae play a pivotal role in the stability of marine environments. However, the toxicity of those short-chain PFAS was lack of investigation. Therefore, we chose 4C PFAS perfluorobutanoic acid (PFBA) and the marine model diatom Thalassiosira pseudonana as research targets, comprehensively studied the toxicity of PFBA to T. pseudonana in terms of the population growth, photosynthetic physiology and oxidative stress. Our results characterized the inhibited growth, inhibited photosynthetic parameters, increased reactive oxygen species (ROS) levels and activated antioxidant system under PFBA exposure. Further transcriptome analysis revealed the underlying molecular mechanisms: photosynthetic genes were slightly down-regulated and the expression of oxidative stress-related genes was enhanced; significant up-regulation of genes related to the DNA excision repair and replication-coupled DNA repair pathways; the expression of carbon metabolisms-related genes was increased, including the Calvin cycle, glycolysis, pentose phosphate pathway, tricarboxylic acid (TCA) cycle and fatty acid biosynthesis, that could provide sufficient energy for the recovery processes of microalgal cells. This study elucidated the underlying toxic mechanisms of PFBA on phytoplankton, and provided novel insights for assessing the environmental risks of PFAS.
Collapse
Affiliation(s)
- Jiayi Shi
- Haide College, Major of Biotechnology, Ocean University of China, Qingdao 266100, China.
| | - Mengyang Hu
- Haide College, Major of Biotechnology, Ocean University of China, Qingdao 266100, China
| | - Zhilin Xia
- Haide College, Major of Biotechnology, Ocean University of China, Qingdao 266100, China
| | - Jirong Zhang
- Haide College, Major of Biotechnology, Ocean University of China, Qingdao 266100, China
| | - Ziniu Wang
- Haide College, Major of Biotechnology, Ocean University of China, Qingdao 266100, China
| | - Luying Li
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao 266003, China
| | - Yan Zhao
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao 266071, China.
| |
Collapse
|
2
|
Dorrell RG, Zhang Y, Liang Y, Gueguen N, Nonoyama T, Croteau D, Penot-Raquin M, Adiba S, Bailleul B, Gros V, Pierella Karlusich JJ, Zweig N, Fernie AR, Jouhet J, Maréchal E, Bowler C. Complementary environmental analysis and functional characterization of lower glycolysis-gluconeogenesis in the diatom plastid. THE PLANT CELL 2024; 36:3584-3610. [PMID: 38842420 PMCID: PMC11371179 DOI: 10.1093/plcell/koae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/14/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
Organic carbon fixed in chloroplasts through the Calvin-Benson-Bassham Cycle can be diverted toward different metabolic fates, including cytoplasmic and mitochondrial respiration, gluconeogenesis, and synthesis of diverse plastid metabolites via the pyruvate hub. In plants, pyruvate is principally produced via cytoplasmic glycolysis, although a plastid-targeted lower glycolytic pathway is known to exist in non-photosynthetic tissue. Here, we characterized a lower plastid glycolysis-gluconeogenesis pathway enabling the direct interconversion of glyceraldehyde-3-phosphate and phospho-enol-pyruvate in diatoms, ecologically important marine algae distantly related to plants. We show that two reversible enzymes required to complete diatom plastid glycolysis-gluconeogenesis, Enolase and bis-phosphoglycerate mutase (PGAM), originated through duplications of mitochondria-targeted respiratory isoforms. Through CRISPR-Cas9 mutagenesis, integrative 'omic analyses, and measured kinetics of expressed enzymes in the diatom Phaeodactylum tricornutum, we present evidence that this pathway diverts plastid glyceraldehyde-3-phosphate into the pyruvate hub, and may also function in the gluconeogenic direction. Considering experimental data, we show that this pathway has different roles dependent in particular on day length and environmental temperature, and show that the cpEnolase and cpPGAM genes are expressed at elevated levels in high-latitude oceans where diatoms are abundant. Our data provide evolutionary, meta-genomic, and functional insights into a poorly understood yet evolutionarily recurrent plastid metabolic pathway.
Collapse
Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris-Seine (IBPS), CNRS, INSERM, Sorbonne Université, Paris 75005, France
| | - Youjun Zhang
- Department of Plant Metabolomics, Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Central Plant Metabolism Group, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Liang
- Center of Deep Sea Research, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Mineral Resources, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Nolwenn Gueguen
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Tomomi Nonoyama
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Dany Croteau
- Institut de Biologie Physico-Chimique (IBPC), Université PSL, Paris 75005, France
| | - Mathias Penot-Raquin
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
- Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris-Seine (IBPS), CNRS, INSERM, Sorbonne Université, Paris 75005, France
| | - Sandrine Adiba
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique (IBPC), Université PSL, Paris 75005, France
| | - Valérie Gros
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Juan José Pierella Karlusich
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Nathanaël Zweig
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| | - Alisdair R Fernie
- Department of Plant Metabolomics, Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
- Central Plant Metabolism Group, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, CNRS, University Grenoble Alpes, CEA, INRAE, IRIG, 38000 Grenoble, France
| | - Chris Bowler
- Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016 Paris, France
| |
Collapse
|
3
|
Liu Y, Tian C, Yang Z, Huang C, Jiao K, Yang L, Duan C, Zhang Z, Li G. Effects of Chronic Heat Stress on Growth, Apoptosis, Antioxidant Enzymes, Transcriptomic Profiles, and Immune-Related Genes of Hong Kong Catfish ( Clarias fuscus). Animals (Basel) 2024; 14:1006. [PMID: 38612245 PMCID: PMC11010891 DOI: 10.3390/ani14071006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Chronic heat stress can have detrimental effects on the survival of fish. This study aimed to investigate the impact of prolonged high temperatures on the growth, antioxidant capacity, apoptosis, and transcriptome analysis of Hong Kong catfish (Clarias fuscus). By analyzing the morphological statistics of C. fuscus subjected to chronic high-temperature stress for 30, 60, and 90 days, it was observed that the growth of C. fuscus was inhibited compared to the control group. The experimental group showed a significant decrease in body weight and body length compared to the control group after 60 and 90 days of high-temperature stress (p < 0.05, p < 0.01). A biochemical analysis revealed significant alterations in the activities of three antioxidant enzymes superoxide dismutase activity (SOD); catalase activity (CAT); glutathione peroxidase activity (GPx), the malondialdehyde content (MDA), and the concentrations of serum alkaline phosphatase (ALP); Aspartate aminotransferase (AST); and alanine transaminase (ALT) in the liver. TUNEL staining indicated stronger apoptotic signals in the high-temperature-stress group compared to the control group, suggesting that chronic high-temperature-induced oxidative stress, leading to liver tissue injury and apoptosis. Transcriptome analysis identified a total of 1330 DEGs, with 835 genes being upregulated and 495 genes being downregulated compared to the control group. These genes may be associated with oxidative stress, apoptosis, and immune response. The findings elucidate the growth changes in C. fuscus under chronic high temperature and provide insights into the underlying response mechanisms to a high-temperature environment.
Collapse
Affiliation(s)
- Yong Liu
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (C.T.); (Z.Y.); (K.J.); (L.Y.); (C.D.)
| | - Changxu Tian
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (C.T.); (Z.Y.); (K.J.); (L.Y.); (C.D.)
| | - Zhihua Yang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (C.T.); (Z.Y.); (K.J.); (L.Y.); (C.D.)
| | - Cailin Huang
- Guangxi Introduction and Breeding Center of Aquaculture, Nanning 530001, China; (C.H.); (Z.Z.)
| | - Kaizhi Jiao
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (C.T.); (Z.Y.); (K.J.); (L.Y.); (C.D.)
| | - Lei Yang
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (C.T.); (Z.Y.); (K.J.); (L.Y.); (C.D.)
| | - Cunyu Duan
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (C.T.); (Z.Y.); (K.J.); (L.Y.); (C.D.)
| | - Zhixin Zhang
- Guangxi Introduction and Breeding Center of Aquaculture, Nanning 530001, China; (C.H.); (Z.Z.)
| | - Guangli Li
- Guangdong Research Center on Reproductive Control and Breeding Technology of Indigenous Valuable Fish Species, Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Fisheries College, Guangdong Ocean University, Zhanjiang 524088, China; (Y.L.); (C.T.); (Z.Y.); (K.J.); (L.Y.); (C.D.)
| |
Collapse
|
4
|
Santos JP, Li W, Keller AA, Slaveykova VI. Mercury species induce metabolic reprogramming in freshwater diatom Cyclotella meneghiniana. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133245. [PMID: 38150761 DOI: 10.1016/j.jhazmat.2023.133245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023]
Abstract
Mercury is a hazardous pollutant of global concern. While advances have been made in identifying the detrimental effects caused by Hg species in phytoplankton, knowledge gaps remain regarding the metabolomic perturbations induced by inorganic mercury (Hg(II)) and monomethylmercury (MeHg) in these organisms. Diatoms represent a major phytoplankton group essential in various global biogeochemical cycles. The current study combined targeted metabolomics, bioaccumulation, and physiological response assays to investigate metabolic perturbations in diatom Cyclotella meneghiniana exposed for 2 h to nanomolar concentrations of Hg(II) and MeHg. Our findings highlight that such exposures induce reprogramming of the metabolism of amino acids, nucleotides, fatty acids, carboxylic acids and antioxidants. These alterations were primarily mercury-species dependent. MeHg exposure induced more pronounced reprogramming of the metabolism of diatoms than Hg(II), which led to less pronounced effects on ROS generation, membrane permeability and chlorophyll concentrations. Hg(II) treatments presented distinct physiological responses, with more robust metabolic perturbations at higher exposures. The present study provides first-time insights into the main metabolic alterations in diatom C. meneghiniana during short-term exposure to Hg species, deepening our understanding of the molecular basis of these perturbations.
Collapse
Affiliation(s)
- João P Santos
- University of Geneva, Faculty of Sciences, Earth and Environment Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Environmental Biogeochemistry and Ecotoxicology, 66 Blvd Carl-Vogt, CH 1211 Geneva, Switzerland.
| | - Weiwei Li
- Bren School of Environmental Science & Management, University of California, Santa Barbara, CA 93106-5131, United States
| | - Arturo A Keller
- Bren School of Environmental Science & Management, University of California, Santa Barbara, CA 93106-5131, United States
| | - Vera I Slaveykova
- University of Geneva, Faculty of Sciences, Earth and Environment Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Environmental Biogeochemistry and Ecotoxicology, 66 Blvd Carl-Vogt, CH 1211 Geneva, Switzerland.
| |
Collapse
|
5
|
Schoenmakers LLJ, Reydon TAC, Kirschning A. Evolution at the Origins of Life? Life (Basel) 2024; 14:175. [PMID: 38398684 PMCID: PMC10890241 DOI: 10.3390/life14020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.
Collapse
Affiliation(s)
- Ludo L. J. Schoenmakers
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI), 3400 Klosterneuburg, Austria
| | - Thomas A. C. Reydon
- Institute of Philosophy, Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, 30159 Hannover, Germany;
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany;
| |
Collapse
|
6
|
Wang M, Chen S, Li S, Zhang J, Sun Y, Wang C, Ni D. Enhancement of nitrogen cycling and functional microbial flora by artificial inoculation of biological soil crusts in sandy soils of highway slopes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:4400-4411. [PMID: 38102430 DOI: 10.1007/s11356-023-31461-0] [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: 09/14/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
Biological soil crusts (BSCs) are common in arid and semi-arid ecosystems and enhance soil stability and fertility. Highway slopes severely deplete the soil ecological structure and soil nutrients, hindering plant survival. The construction of highway slope BSCs under human intervention is critical to ensure the long-term stable operation of the slope ecosystem. This study investigated the variation rules and interaction mechanisms between soil nutrients and microbial communities in the subsoil BSCs on highway slopes. Bacterial 16S rRNA high-throughput sequencing was employed to investigate the dynamic compositional changes in the microbial community and perform critical metabolic predictive analyses of functional bacteria. This study revealed that the total soil nitrogen increased significantly from 0.557 to 0.864 g/kg after artificial inoculation with desert Phormidium tenue and Scytonema javanicum. Actinobacteria (44-48%) and Proteobacteria (28-31%) were the dominant phyla in all samples. The abundance of Cyanobacteria, Cytophagaceae, and Chitinophagaceae increased significantly after inoculation. PICRUST analysis showed that the main metabolic pathways of soil microorganisms on highway slopes included cofactor and vitamin, nucleotide, and amino acid metabolisms. These findings suggest that the artificial inoculation with Phormidium tenue and Scytonema javanicum could alter soil microbial distribution to promote soil development on highway slopes toward nutrient accumulation.
Collapse
Affiliation(s)
- Mengyan Wang
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
| | - Sibao Chen
- Key Laboratory of Changjiang Regulation and Protection of Ministry of Water Resources, Changjiang Institude of Survey Planning Design and Research, Wuhan, 430010, China
| | - Shuangshuang Li
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Jianhong Zhang
- China International Engineering Consulting Corporation, Ltd., Beijing, 100048, China
| | - Yingxue Sun
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
| | - Chun Wang
- State Environmental Protection Key Laboratory of Food Chain Pollution Control, School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China.
- Key Laboratory of Road Traffic Environmental Protection Technology, Ministry of Transport, Beijing, 100088, China.
| | - Dong Ni
- Key Laboratory of Road Traffic Environmental Protection Technology, Ministry of Transport, Beijing, 100088, China
| |
Collapse
|
7
|
Zhang S, Zhao B, Zhang X, Wu F, Zhao Q. The Metabolomics Response of Solanum melongena L. Leaves to Various Forms of Pb. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2911. [PMID: 37999265 PMCID: PMC10675538 DOI: 10.3390/nano13222911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 11/25/2023]
Abstract
Due to activities like mining and smelting, lead (Pb) enters the atmosphere in various forms in coarse and fine particles. It enters plants mainly through leaves, and goes up the food chain. In this study, PbXn (nano-PbS, mic-PbO and PbCl2) was applied to eggplant (Solanum melongena L.) leaves, and 379 differential metabolites were identified and analyzed in eggplant leaves using liquid chromatography-mass spectrometry. Multivariate statistical analysis revealed that all three Pb treatments significantly altered the metabolite profile. Compared with nano-PbS, mic-PbO and PbCl2 induced more identical metabolite changes. However, the alterations in metabolites related to the TCA cycle and pyrimidine metabolism, such as succinic acid, citric acid and cytidine, were specific to PbCl2. The number of differential metabolites induced by mic-PbO and PbCl2 was three times that of nano-PbS, even though the amount of nano-PbS absorbed by leaves was ten times that of PbO and seven times that of PbCl2. This suggests that the metabolic response of eggplant leaves to Pb is influenced by both concentration and form. This study enhances the current understanding of plants' metabolic response to Pb, and demonstrates that the metabolomics map provides a more comprehensive view of a plant's response to specific metals.
Collapse
Affiliation(s)
- Siyu Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (S.Z.); (B.Z.); (X.Z.)
| | - Bing Zhao
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (S.Z.); (B.Z.); (X.Z.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuejiao Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (S.Z.); (B.Z.); (X.Z.)
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China;
| | - Qing Zhao
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (S.Z.); (B.Z.); (X.Z.)
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
8
|
Naz S, Liu P, Farooq U, Ma H. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microb Cell Fact 2023; 22:161. [PMID: 37612753 PMCID: PMC10464499 DOI: 10.1186/s12934-023-02178-z] [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: 06/07/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023] Open
Abstract
Regulation of amino acid's biosynthetic pathway is of significant importance to maintain homeostasis and cell functions. Amino acids regulate their biosynthetic pathway by end-product feedback inhibition of enzymes catalyzing committed steps of a pathway. Discovery of new feedback resistant enzyme variants to enhance industrial production of amino acids is a key objective in industrial biotechnology. Deregulation of feedback inhibition has been achieved for various enzymes using in vitro and in silico mutagenesis techniques. As enzyme's function, its substrate binding capacity, catalysis activity, regulation and stability are dependent on its structural characteristics, here, we provide detailed structural analysis of all feedback sensitive enzyme targets in amino acid biosynthetic pathways. Current review summarizes information regarding structural characteristics of various enzyme targets and effect of mutations on their structures and functions especially in terms of deregulation of feedback inhibition. Furthermore, applicability of various experimental as well as computational mutagenesis techniques to accomplish feedback resistance has also been discussed in detail to have an insight into various aspects of research work reported in this particular field of study.
Collapse
Affiliation(s)
- Sadia Naz
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Pi Liu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Islamabad, 22060, Pakistan
| | - Hongwu Ma
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| |
Collapse
|
9
|
Zhao S, Zhao X, Li Y, Zhang R, Zhao Y, Fang H, Li W. Impact of altered groundwater depth on soil microbial diversity, network complexity and multifunctionality. Front Microbiol 2023; 14:1214186. [PMID: 37601343 PMCID: PMC10434790 DOI: 10.3389/fmicb.2023.1214186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
Understanding the effects of groundwater depth on soil microbiota and multiple soil functions is essential for ecological restoration and the implementation of groundwater conservation. The current impact of increased groundwater levels induced by drought on soil microbiota and multifunctionality remains ambiguous, which impedes our understanding of the sustainability of water-scarce ecosystems that heavily rely on groundwater resources. This study investigated the impacts of altered groundwater depths on soil microbiota and multifunctionality in a semi-arid region. Three groundwater depth levels were studied, with different soil quality and soil moisture at each level. The deep groundwater treatment had negative impacts on diversity, network complexity of microbiota, and the relationships among microbial phylum unites. Increasing groundwater depth also changed composition of soil microbiota, reducing the relative abundance of dominant phyla including Proteobacteria and Ascomycota. Increasing groundwater depth led to changes in microbial community characteristics, which are strongly related to alterations in soil multifunctionality. Overall, our results suggest that groundwater depth had a strongly effect on soil microbiota and functionality.
Collapse
Affiliation(s)
- Siteng Zhao
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueyong Zhao
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Yulin Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Rui Zhang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Naiman Desertification Research Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Tongliao, China
| | - Yanming Zhao
- Tongliao Hydrology and Water Resources Sub-center, Tongliao, China
| | - Hong Fang
- Tongliao Hydrology and Water Resources Sub-center, Tongliao, China
| | - Wenshuang Li
- Tongliao Hydrology and Water Resources Sub-center, Tongliao, China
| |
Collapse
|
10
|
Kabir MA, Iqbal MM, Nandi SK, Khanam M, Sumon MAA, Tahiluddin AB, Kari ZA, Wei LS, Téllez-Isaías G. Comparative study of ovarian development in wild and captive-reared long-whiskered Sperata aor (Hamilton, 1822). BMC ZOOL 2023; 8:10. [PMID: 37488631 PMCID: PMC10364359 DOI: 10.1186/s40850-023-00172-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 07/26/2023] Open
Abstract
Long-whiskered catfish Sperata aor is a freshwater catfish known for its supreme flesh quality and fast growth, whose captive-reared broodstock denotes a difficult challenge for aquaculture. The reproductive dysfunctions in long-whiskered catfish raised in tank conditions were observed by comparing tissue biochemical composition and ovarian histology of wild female broodstock. Sixty (60) female broodstocks were used in the current study, consisting of 30 reared at sandy-muddy soil tank bottoms in captive conditions and 30 wild individuals collected from the haor basin during the breeding season. The fish reproductive state was investigated using the biometric and reproductive parameters, biochemical composition and levels of amino acids in the different tissues, and histological analysis of ovarian development. Results revealed that the biometrical parameters of wild and captive female broodstocks exhibited no remarkable difference (p > 0.05). Nevertheless, the wild fish had remarkably higher (p < 0.05) GSI (8.73%), oocyte weight (0.45 mg/egg), and ripeness (27.08%) in comparison with captive-reared broodstock. The total length and body weight, body weight and ovary weight, ovipositor diameter and ovary weight, and GSI and HSI displayed a positive relationship with R2 = 1, R2 = 1, R2 = 0.993, and R2 = 0.973, respectively, for wild broodstock, while R2 = 0.994, R2 = 0.806, R2 = 0.804, and R2 = 0.896, respectively, for captive broodstock. Additionally, the proximate composition in oocytes and liver tissues in both broodstocks did not differ significantly (p > 0.05). However, two essential amino acids (EAA), i.e., lysine and phenylalanine, and two non-essential amino acids, i.e., glutamic acid and glycine, were highly significant differences (p < 0.05) in the oocytes and liver of wild broodstock compared to the captive-reared broodstock. On the other hand, the EAA, e.g., isoleucine, threonine, leucine, and arginine, were highly dominated in both wild and captive female brood oocytes and liver. The ovarian histological slides from each fish group showed three oocytes developmental stages that indicated the asynchronous-reproductive ovarian oocytes of this fish. This study may be useful to fully understand the factors affecting the spawning and reproduction of S. aor broodstock, crucial for management in captive conditions as well as conservation and protection for sustainable aquaculture management of S. aor.
Collapse
Affiliation(s)
- Muhammad Anamul Kabir
- Department of Aquaculture, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
- Advanced Livestock and Aquaculture Research Group, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, Jeli, 17600, Kelantan, Malaysia.
| | - Mohammed Mahbub Iqbal
- Department of Fish Biology and Genetics, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Shishir Kumar Nandi
- Department of Aquaculture, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Mahbuba Khanam
- Department of Aquaculture, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Md Afsar Ahmed Sumon
- Marine Biology Department, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Albaris B Tahiluddin
- College of Fisheries, Mindanao State University-Tawi-Tawi College of Technology and Oceanography, Sanga-Sanga, Bongao, 7500, Tawi-Tawi, Philippines
| | - Zulhisyam Abdul Kari
- Department of Agricultural Sciences, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, Jeli, 17600, Kelantan, Malaysia.
- Advanced Livestock and Aquaculture Research Group, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, Jeli, 17600, Kelantan, Malaysia.
| | - Lee Seong Wei
- Department of Agricultural Sciences, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, Jeli, 17600, Kelantan, Malaysia
- Advanced Livestock and Aquaculture Research Group, Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli Campus, Jeli, 17600, Kelantan, Malaysia
| | | |
Collapse
|
11
|
Feltracco M, Zangrando R, Barbaro E, Becagli S, Park KT, Vecchiato M, Caiazzo L, Traversi R, Severi M, Barbante C, Gambaro A. Characterization of free L- and D-amino acids in size-segregated background aerosols over the Ross Sea, Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163070. [PMID: 36990237 DOI: 10.1016/j.scitotenv.2023.163070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/10/2023] [Accepted: 03/22/2023] [Indexed: 05/17/2023]
Abstract
The study of airborne chemical markers is crucial for identifying sources of aerosols, and their atmospheric processes of transport and transformation. The investigation of free amino acids and their differentiation between the L- and D- enantiomers are even more important to understand their sources and atmospheric fate. Aerosol samples were collected with a high-volume sampler with cascade impactor at Mario Zucchelli Station (MZS) on the coast of the Ross Sea (Antarctica) for two summer campaigns (2018/19 and 2019/20). The total mean concentration of free amino acids in PM10 was 4 ± 2 pmol m-3 for both campaigns and most of free amino acids were distributed in fine particles. The coarse mode of airborne D-Alanine and dimethylsufoniopropionate in seawater showed a similar trend during both Antarctic campaigns. Thus, the study of D/L Ala ratio in fine, coarse and PM10 fractions indicated the microlayer as the local source. This paper demonstrated that free amino acids follow the trend of DMS and MSA release occurred in the Ross Sea, confirming their applicability as markers for phytoplankton bloom also in paleoclimatic studies.
Collapse
Affiliation(s)
- Matteo Feltracco
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino, 155 - 30172 Venice Mestre (VE), Italy.
| | - Roberta Zangrando
- Institute of Polar Sciences, National Research Council (CNR-ISP), Via Torino, 155 - 30172 Venice Mestre (VE), Italy; Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino, 155 - 30172 Venice Mestre (VE), Italy
| | - Elena Barbaro
- Institute of Polar Sciences, National Research Council (CNR-ISP), Via Torino, 155 - 30172 Venice Mestre (VE), Italy; Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino, 155 - 30172 Venice Mestre (VE), Italy
| | - Silvia Becagli
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy; Institute of Polar Sciences, National Research Council (CNR-ISP), Via Torino, 155 - 30172 Venice Mestre (VE), Italy
| | - Ki-Tae Park
- Korea Polar Research Institute (KOPRI), Incheon 21990, South Korea
| | - Marco Vecchiato
- Institute of Polar Sciences, National Research Council (CNR-ISP), Via Torino, 155 - 30172 Venice Mestre (VE), Italy; Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino, 155 - 30172 Venice Mestre (VE), Italy
| | - Laura Caiazzo
- ENEA Laboratory of Observations and Measurements for the Environment and Climate, Rome, Italy
| | - Rita Traversi
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy; Institute of Polar Sciences, National Research Council (CNR-ISP), Via Torino, 155 - 30172 Venice Mestre (VE), Italy
| | - Mirko Severi
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy; Institute of Polar Sciences, National Research Council (CNR-ISP), Via Torino, 155 - 30172 Venice Mestre (VE), Italy
| | - Carlo Barbante
- Institute of Polar Sciences, National Research Council (CNR-ISP), Via Torino, 155 - 30172 Venice Mestre (VE), Italy; Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino, 155 - 30172 Venice Mestre (VE), Italy
| | - Andrea Gambaro
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino, 155 - 30172 Venice Mestre (VE), Italy; Institute of Polar Sciences, National Research Council (CNR-ISP), Via Torino, 155 - 30172 Venice Mestre (VE), Italy
| |
Collapse
|
12
|
Liu Y, Ma C, Sun J. Integrated FT-ICR MS and metabolome reveals diatom-derived organic matter by bacterial transformation under warming and acidification. iScience 2023; 26:106812. [PMID: 37213222 PMCID: PMC10197009 DOI: 10.1016/j.isci.2023.106812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/21/2023] [Accepted: 05/01/2023] [Indexed: 05/23/2023] Open
Abstract
Bacterial transformation and processing of diatom-derived organic matter (OM) is extremely important for the cycling of production and energy in marine ecosystems; this process contributes to the production of microbial food webs. In this study, a cultivable bacterium (Roseobacter sp. SD-R1) from the marine diatom Skeletonema dohrnii were isolated and identified. A combined Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS)/untargeted metabolomics approach was used to synthesize the results of bacterial transformation with dissolved OM (DOM) and lysate OM (LOM) under warming and acidification through laboratory experiments. Roseobacter sp. SD-R1 had different preferences for the conversion of molecules in S. dohrnii-derived DOM and LOM treatments. The effects of warming and acidification contribute to the increased number and complexity of molecules of carbon, hydrogen, oxygen, nitrogen, and sulfur after the bacterial transformation of OM. The chemical complexity generated by bacterial metabolism provides new insights into the mechanisms that shape OM complexity.
Collapse
Affiliation(s)
- Yang Liu
- Institute for Advance Marine Research, China University of Geosciences, Guangzhou 511462, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Chao Ma
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Jun Sun
- Institute for Advance Marine Research, China University of Geosciences, Guangzhou 511462, China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
- Corresponding author
| |
Collapse
|
13
|
Mecha E, Alves ML, Bento da Silva A, Pereira AB, Rubiales D, Vaz Patto MC, Bronze MR. High Inter- and Intra- Diversity of Amino Acid Content and Protein Digestibility Disclosed in Five Cool Season Legume Species with a Growing Market Demand. Foods 2023; 12:foods12071383. [PMID: 37048201 PMCID: PMC10093753 DOI: 10.3390/foods12071383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Legumes have been sought as alternative protein sources to ensure food security and environmental sustainability. Characterizing their protein content and quality, including in underutilized grain legumes, e.g., grass pea, gives value to the legumes' underexplored variability. To fill the gap of knowledge in legumes' protein quality, for the first time, five extensive collections of cool season grain legumes were cropped under the same environmental conditions and further analyzed. Multivariate analysis showed the existent intra- and inter-species variability. The legume species with the highest protein content, grass pea, Lathyrus sativus (LS), was not the one with the overall highest individual amino acids content and in vitro protein digestibility. With these last characteristics lentil, Lens culinaris (LC), was highlighted. The highest average values of arginine (Arg), glutamic acid (Glu), and threonine (Thr) were found in LS and Vicia faba (VF). Cicer arietinum (CA) stood out as the species with the highest values of Thr and methionine (Met). Regarding the in vitro protein digestibility (IVPD), LC, followed by Pisum sativum (PS) and LS, were the legume species with the highest values. Ultimately, this study bought to the fore legume species that are not commonly used in western diets but have high adaptability to the European agricultural systems.
Collapse
Affiliation(s)
- Elsa Mecha
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Av. da República, Apartado 12, 2781-901 Oeiras, Portugal
| | - Mara Lisa Alves
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Andreia Bento da Silva
- Faculdade de Farmácia, Universidade de Lisboa, Av. das Forças Armadas, 1649-019 Lisboa, Portugal
| | - Ana Bárbara Pereira
- iBET, Instituto de Biologia Experimental e Tecnológica, Av. da República, Apartado 12, 2781-901 Oeiras, Portugal
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Avda Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Maria Carlota Vaz Patto
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Maria Rosário Bronze
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
- iBET, Instituto de Biologia Experimental e Tecnológica, Av. da República, Apartado 12, 2781-901 Oeiras, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Av. das Forças Armadas, 1649-019 Lisboa, Portugal
| |
Collapse
|
14
|
Hano T, Tomaru Y. Chronological age-related metabolome responses in the dinoflagellate Karenia mikimotoi, can predict future bloom demise. Commun Biol 2023; 6:273. [PMID: 36922623 PMCID: PMC10017670 DOI: 10.1038/s42003-023-04646-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Karenia mikimotoi is a common harmful algal bloom (HAB)-forming dinoflagellate and has caused severe financial loss in aquaculture. There are limited metabolomic studies on dinoflagellate biology. Here, we examined alterations in metabolic profiles over the growth curve of K. mikimotoi under nitrogen or phosphorus deficiency and further explored a key criterion for the diagnosis of late stationary phase to identify when the dinoflagellate cells will enter bloom demise. The results demonstrate the differential expression of metabolites for coping with chronological aging or nutrient deprivation. Furthermore, an increase in the glucose to glycine ratio in the late stationary phase was indicative of dinoflagellate cells entering bloom demise; this was also detected in the cultured diatom, Chaetoceros tenuissimus, indicating that this may be the general criterion for phytoplankton species. Our findings provide insights regarding chronological aging and the criterion for the prediction of phytoplankton bloom demise.
Collapse
Affiliation(s)
- Takeshi Hano
- Environment Conservation Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan.
| | - Yuji Tomaru
- Environment Conservation Division, Fisheries Technology Institute, National Research and Development Agency, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan
| |
Collapse
|
15
|
Velička A, Tarasevičienė Ž, Hallmann E, Kieltyka-Dadasiewicz A. Impact of Foliar Application of Amino Acids on Essential Oil Content, Odor Profile, and Flavonoid Content of Different Mint Varieties in Field Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212938. [PMID: 36365392 PMCID: PMC9731322 DOI: 10.3390/plants11212938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 05/31/2023]
Abstract
Mint is an industrial plant that is a good source of essential oil and many phenolic compounds that have several positive benefits to human health and can be used to prevent the development of many diseases. The aim of this research was to investigate the possibility of increasing essential oil and flavonoid content, changing the chemical composition of these compounds in different mint cultivars under foliar application with precursors (phenylalanine, tryptophan, and tyrosine) at two concentrations, 100 and 200 mg L-1, to enable the possibilities for wider use of these plants when they are grown in field conditions. Spraying with phenylalanine at 100 mg L-1 concentration increased essential oil content in Mentha piperita 'Granada' plants by 0.53 percentage units. Foliar application with tyrosine solutions at 100 mg L-1 concentration most effectively influenced the essential oil odor profile Mentha spicata 'Crispa'. The highest number of total flavonoids was in Mentha piperita 'Swiss' sprayed with tyrosine at 100 mg L-1 concentration. The flavonoid content depended on the mint cultivar, amino acids, and their concentration. The results showed that the effect of amino acid solutions on different secondary metabolites' quantitative and qualitative composition differed depending on the mint cultivar; therefore, amino acids and their concentrations must be selected based on the cultivar they are targeting.
Collapse
Affiliation(s)
- Aloyzas Velička
- Department of Plants Biology and Food Science, Faculty of Agronomy, Agriculture Academy Vytautas Magnus University, Donelaicio STR. 52, LT-44248 Kaunas, Lithuania
| | - Živilė Tarasevičienė
- Department of Plants Biology and Food Science, Faculty of Agronomy, Agriculture Academy Vytautas Magnus University, Donelaicio STR. 52, LT-44248 Kaunas, Lithuania
| | - Ewelina Hallmann
- Department of Functional and Organic Food, Institute of Human Nutrition Sciences, Warsaw University of Life Sciences, Nowoursynowska 159 c, 02-776 Warsaw, Poland
- Bioeconomy Research Institute, Agriculture Academy, Vytautas Magnus University, K. Donelaicio Str. 58, LT-44248 Kaunas, Lithuania
| | - Anna Kieltyka-Dadasiewicz
- Department of Plant Production Technology and Commodity, University of Life Sciences in Lublin, Akademicka 15, 20-950 Lublin, Poland
| |
Collapse
|
16
|
Abstract
α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.
Collapse
Affiliation(s)
- Andreas Kirschning
- Institute of Organic ChemistryLeibniz University HannoverSchneiderberg 1B30167HannoverGermany
| |
Collapse
|
17
|
Kong W, Wei X, Wu Y, Shao M, Zhang Q, Sadowsky MJ, Ishii S, Reich PB, Wei G, Jiao S, Qiu L, Liu L. Afforestation can lower microbial diversity and functionality in deep soil layers in a semiarid region. GLOBAL CHANGE BIOLOGY 2022; 28:6086-6101. [PMID: 35808859 DOI: 10.1111/gcb.16334] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Afforestation is an effective approach to rehabilitate degraded ecosystems, but often depletes deep soil moisture. Presently, it is not known how an afforestation-induced decrease in moisture affects soil microbial community and functionality, hindering our ability to understand the sustainability of the rehabilitated ecosystems. To address this issue, we examined the impacts of 20 years of afforestation on soil bacterial community, co-occurrence pattern, and functionalities along vertical profile (0-500 cm depth) in a semiarid region of China's Loess Plateau. We showed that the effects of afforestation with a deep-rooted legume tree on cropland were greater in deep than that of in top layers, resulting in decreased bacterial beta diversity, more responsive bacterial taxa and functional groups, increased homogeneous selection, and decreased network robustness in deep soils (120-500 cm). Organic carbon and nitrogen decomposition rates and multifunctionality also significantly decreased by afforestation, and microbial carbon limitation significantly increased in deep soils. Moreover, changes in microbial community and functionality in deep layer was largely related to changes in soil moisture. Such negative impacts on deep soils should be fully considered for assessing afforestation's eco-environment effects and for the sustainability of ecosystems because deep soils have important influence on forest ecosystems in semiarid and arid climates.
Collapse
Affiliation(s)
- Weibo Kong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaorong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Mingan Shao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, China
| | - Qian Zhang
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Michael J Sadowsky
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, USA
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter B Reich
- Department of Forest Resources, University of Minnesota, St. Paul, Minnesota, USA
- Institute for Global Change Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gehong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
| | - Shuo Jiao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
| | - Liping Qiu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, China
| | - Liling Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, China
| |
Collapse
|
18
|
Du Z, Lin W, Zhu J, Li J. Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus. PeerJ 2022; 10:e13689. [PMID: 35811808 PMCID: PMC9266588 DOI: 10.7717/peerj.13689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 06/16/2022] [Indexed: 01/17/2023] Open
Abstract
Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
Collapse
Affiliation(s)
- Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang, China
| | - Weida Lin
- Taizhou Vocational College of Science and Technology, Taizhou, Zhejiang, China
| | - Jinxing Zhu
- Suichang County Bureau of Agriculture and Rural Affairs, Suichang, Zhejiang, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang, China
| |
Collapse
|
19
|
Zhang M, Li Y, Mu Q, Feng F, Yu X, Ge J, Zhang Y, Nie J. Effects of chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB. CHEMOSPHERE 2022; 297:134189. [PMID: 35248589 DOI: 10.1016/j.chemosphere.2022.134189] [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: 11/30/2021] [Revised: 02/12/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Many microorganisms have been reported to degrade organic pollutants in the environment and plants, however, the specific information about the effect of organic pollutants on the metabolism of microorganisms is poorly investigated. In the present study, the effect of the pesticide chlorpyrifos on the metabolic profiling of Bacillus megaterium strain RRB was investigated using metabolomics. Our data show that chlorpyrifos acting as an energy source was readily concentrated in the strain RRB from the culture medium. During early cultivation, the shift in energy sources from tryptic soy broth to chlorpyrifos may temporarily cause the strain RRB to enter the starvation stage, where some synthesis-related amino acids and intermediates in the pathways of TCA cycle and pyridoxine metabolism were decreased. The increase of nucleotides and lysine may help the strain RRB cope with the starvation stage. During later cultivation, many metabolites including organic acids, nucleosides and sugar phosphates were gradually accumulated, which indicates that chlorpyrifos could be utilized by the stain RRB to generate metabolites bacteria needed. In addition, arginine acting as a nitrogen-storage amino acid was gradually decreased with later cultivation, suggesting that chlorpyrifos could not provide enough nitrogen for bacteria.
Collapse
Affiliation(s)
- Mingxia Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Yong Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China; School of Food and Biological Engineering, Jiangsu University, 301 Zhenjiang City University Road, Zhenjiang, 212001, China.
| | - Qi'e Mu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China; Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Fayun Feng
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Xiangyang Yu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Jing Ge
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
| | - Yun Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China
| | - Jinfang Nie
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, 541004, China.
| |
Collapse
|
20
|
Jiménez-Gómez I, Valdés-Muñoz G, Moreno-Ulloa A, Pérez-Llano Y, Moreno-Perlín T, Silva-Jiménez H, Barreto-Curiel F, Sánchez-Carbente MDR, Folch-Mallol JL, Gunde-Cimerman N, Lago-Lestón A, Batista-García RA. Surviving in the Brine: A Multi-Omics Approach for Understanding the Physiology of the Halophile Fungus Aspergillus sydowii at Saturated NaCl Concentration. Front Microbiol 2022; 13:840408. [PMID: 35586858 PMCID: PMC9108488 DOI: 10.3389/fmicb.2022.840408] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/07/2022] [Indexed: 11/30/2022] Open
Abstract
Although various studies have investigated osmoadaptations of halophilic fungi to saline conditions, only few analyzed the fungal mechanisms occurring at saturated NaCl concentrations. Halophilic Aspergillus sydowii is a model organism for the study of molecular adaptations of filamentous fungi to hyperosmolarity. For the first time a multi-omics approach (i.e., transcriptomics and metabolomics) was used to compare A. sydowii at saturated concentration (5.13 M NaCl) to optimal salinity (1 M NaCl). Analysis revealed 1,842 genes differentially expressed of which 704 were overexpressed. Most differentially expressed genes were involved in metabolism and signal transduction. A gene ontology multi-scale network showed that ATP binding constituted the main network node with direct interactions to phosphorelay signal transduction, polysaccharide metabolism, and transferase activity. Free amino acids significantly decreased and amino acid metabolism was reprogrammed at 5.13 M NaCl. mRNA transcriptional analysis revealed upregulation of genes involved in methionine and cysteine biosynthesis at extreme water deprivation by NaCl. No modifications of membrane fatty acid composition occurred. Upregulated genes were involved in high-osmolarity glycerol signal transduction pathways, biosynthesis of β-1,3-glucans, and cross-membrane ion transporters. Downregulated genes were related to the synthesis of chitin, mannose, cell wall proteins, starvation, pheromone synthesis, and cell cycle. Non-coding RNAs represented the 20% of the total transcripts with 7% classified as long non-coding RNAs (lncRNAs). The 42% and 69% of the total lncRNAs and RNAs encoding transcription factors, respectively, were differentially expressed. A network analysis showed that differentially expressed lncRNAs and RNAs coding transcriptional factors were mainly related to the regulation of metabolic processes, protein phosphorylation, protein kinase activity, and plasma membrane composition. Metabolomic analyses revealed more complex and unknown metabolites at saturated NaCl concentration than at optimal salinity. This study is the first attempt to unravel the molecular ecology of an ascomycetous fungus at extreme water deprivation by NaCl (5.13 M). This work also represents a pioneer study to investigate the importance of lncRNAs and transcriptional factors in the transcriptomic response to high NaCl stress in halophilic fungi.
Collapse
Affiliation(s)
- Irina Jiménez-Gómez
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Gisell Valdés-Muñoz
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Aldo Moreno-Ulloa
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Yordanis Pérez-Llano
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Tonatiuh Moreno-Perlín
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Hortencia Silva-Jiménez
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Ensenada, Mexico
| | | | | | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Asunción Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
- *Correspondence: Ramón Alberto Batista-García, ;
| |
Collapse
|
21
|
An F, Niu Z, Liu T, Su Y. Succession of soil bacterial community along a 46-year choronsequence artificial revegetation in an arid oasis-desert ecotone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152496. [PMID: 34968610 DOI: 10.1016/j.scitotenv.2021.152496] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
How the bacterial community structure and potential metabolic functions will change after revegetation in arid desert ecosystems is still unknown. We used high-throughput pyrosequencing to explore changes in soil bacterial diversity, structure and metabolic pathways, and the key driving factors along a chronosequence of 46-year Haloxylon ammodendron revegetation in an oasis-desert ecotone in the northwestern China. Our results indicated that establishment of H. ammodendron on shifting sand dunes significantly changed the structure of bacterial communities and increased their diversity and richness. The main dominant phyla were Actinobacteria (32.1-41.3%) and Proteobacteria (19.2-27.0%); in that, α-Proteobacteria (16.4-20.7%) were the most abundant Proteobacteria. Kocuria coexisted at different succession stage after year 0, and their relative abundance ranged from 3.8-9.0%. Principal coordinates analysis (PCoA) showed that bacterial community from the same revegetation site grouped together and generally separated from each other, indicating that significant shifts in bacterial community structure occurred after revegetation. LEfSe analysis identified unique biomarkers in the soil samples from seven sites. Moreover, PICRUSt analysis indicated similar overall patterns of metabolic pathways in different succession stage. Redundancy analysis (RDA) showed that total carbon, pH and total phosphorus were major abiotic factors driving the structure of bacterial communities, which explained 57.5% of the variation in bacterial communities. Our findings advance the current understanding of plant-soil interactions in the processes of ecological restoration and desertification reversal.
Collapse
Affiliation(s)
- Fangjiao An
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziru Niu
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingna Liu
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongzhong Su
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
| |
Collapse
|
22
|
Duncan RJ, Nielsen DA, Sheehan CE, Deppeler S, Hancock AM, Schulz KG, Davidson AT, Petrou K. Ocean acidification alters the nutritional value of Antarctic diatoms. THE NEW PHYTOLOGIST 2022; 233:1813-1827. [PMID: 34988987 DOI: 10.1111/nph.17868] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/07/2021] [Indexed: 06/14/2023]
Abstract
Primary production in the Southern Ocean is dominated by diatom-rich phytoplankton assemblages, whose individual physiological characteristics and community composition are strongly shaped by the environment, yet knowledge on how diatoms allocate cellular energy in response to ocean acidification (OA) is limited. Understanding such changes in allocation is integral to determining the nutritional quality of diatoms and the subsequent impacts on the trophic transfer of energy and nutrients. Using synchrotron-based Fourier transform infrared microspectroscopy, we analysed the macromolecular content of selected individual diatom taxa from a natural Antarctic phytoplankton community exposed to a gradient of fCO2 levels (288-1263 µatm). Strong species-specific differences in macromolecular partitioning were observed under OA. Large taxa showed preferential energy allocation towards proteins, while smaller taxa increased both lipid and protein stores at high fCO2 . If these changes are representative of future Antarctic diatom physiology, we may expect a shift away from lipid-rich large diatoms towards a community dominated by smaller taxa, but with higher lipid and protein stores than their present-day contemporaries, a response that could have cascading effects on food web dynamics in the Antarctic marine ecosystem.
Collapse
Affiliation(s)
- Rebecca J Duncan
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia
- Department of Arctic Biology, The University Centre in Svalbard, Longyearbyen, 9171, Norway
| | - Daniel A Nielsen
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Cristin E Sheehan
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Stacy Deppeler
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., 7001, Australia
- National Institute of Water and Atmospheric Research, Wellington, 6021, New Zealand
| | - Alyce M Hancock
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tas., 7001, Australia
- Antarctic Gateway Partnership, Battery Point, Tas., 7004, Australia
- Antarctic Climate and Ecosystems Cooperative Research Centre, Hobart, Tas., 7001, Australia
| | - Kai G Schulz
- Centre for Coastal Biogeochemistry, Southern Cross University, East Lismore, NSW, 2480, Australia
| | - Andrew T Davidson
- Antarctic Climate and Ecosystems Cooperative Research Centre, Hobart, Tas., 7001, Australia
- Australian Antarctic Division, Department of the Environment and Energy, Hobart, Tas., 7050, Australia
| | - Katherina Petrou
- School of Life Sciences, University of Technology Sydney, Sydney, NSW, 2007, Australia
| |
Collapse
|
23
|
Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes. Int J Mol Sci 2021; 22:ijms222413332. [PMID: 34948131 PMCID: PMC8706660 DOI: 10.3390/ijms222413332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodinium kawagutii for annotation enabled the characterization of the proteins in P. bahamense. The highest number of annotated hits were obtained from M. algicola and highlighted the contribution of microorganisms associated with P. bahamense. Proteins involved in dimethylsulfoniopropionate (DMSP) degradation such as propionyl CoA synthethase and acryloyl-CoA reductase were identified, suggesting the DMSP cleavage pathway as the preferred route in this dinoflagellate. Most of the annotated proteins were involved in amino acid biosynthesis and carbohydrate degradation and metabolism, indicating the active roles of these molecules in the vegetative stage of P. bahamense. This characterization provides baseline information on the cellular machinery and the molecular basis of the ecophysiology of P. bahamense.
Collapse
|
24
|
Afforestation with Pinus sylvestris var. mongolica remodelled soil bacterial community and potential metabolic function in the Horqin Desert. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
25
|
Ramirez MD, Besser AC, Newsome SD, McMahon KW. Meta‐analysis of primary producer amino acid δ
15
N values and their influence on trophic position estimation. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13678] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew D. Ramirez
- Graduate School of Oceanography University of Rhode Island Narragansett RI USA
| | - Alexi C. Besser
- Department of Biology University of New Mexico Albuquerque NM USA
| | - Seth D. Newsome
- Department of Biology University of New Mexico Albuquerque NM USA
| | - Kelton W. McMahon
- Graduate School of Oceanography University of Rhode Island Narragansett RI USA
| |
Collapse
|
26
|
Toplis B, Bosch C, Schwartz IS, Kenyon C, Boekhout T, Perfect JR, Botha A. The virulence factor urease and its unexplored role in the metabolism of Cryptococcus neoformans. FEMS Yeast Res 2021; 20:5850754. [PMID: 32490521 DOI: 10.1093/femsyr/foaa031] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022] Open
Abstract
Cryptococcal urease is believed to be important for the degradation of exogenous urea that the yeast encounters both in its natural environment and within the human host. Endogenous urea produced by the yeast's own metabolic reactions, however, may also serve as a substrate for the urease enzyme. Using wild-type, urease-deletion mutant and urease-reconstituted strains of Cryptococcus neoformans H99, we studied reactions located up- and downstream from endogenous urea. We demonstrated that urease is important for cryptococcal growth and that, compared to nutrient-rich conditions at 26°C, urease activity is higher under nutrient-limited conditions at 37°C. Compared to cells with a functional urease enzyme, urease-deficient cells had significantly higher intracellular urea levels and also showed more arginase activity, which may act as a potential source of endogenous urea. Metabolic reactions linked to arginase were also affected, since urease-positive and urease-negative cells differed with respect to agmatinase activity, polyamine synthesis, and intracellular levels of proline and reactive oxygen species. Lastly, urease-deficient cells showed higher melanin levels at 26°C than wild-type cells, while the inverse was observed at 37°C. These results suggest that cryptococcal urease is associated with the functioning of key metabolic pathways within the yeast cell.
Collapse
Affiliation(s)
- Barbra Toplis
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
| | - Caylin Bosch
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
| | - Ilan S Schwartz
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Chris Kenyon
- Sexually Transmitted Infection Unit, Institute of Tropical Medicine, 2000 Antwerp, Belgium.,Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, 3584CT Utrecht, The Netherlands.,Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - John R Perfect
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC 27710-1000, North Carolina, USA
| | - Alfred Botha
- Department of Microbiology, Stellenbosch University, Matieland 7602, Stellenbosch, South Africa
| |
Collapse
|
27
|
Li J, Pan K, Tang X, Li Y, Zhu B, Zhao Y. The molecular mechanisms of Chlorella sp. responding to high CO 2: A study based on comparative transcriptome analysis between strains with high- and low-CO 2 tolerance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:144185. [PMID: 33383507 DOI: 10.1016/j.scitotenv.2020.144185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 05/28/2023]
Abstract
High CO2 acclimation for microalgae has attracted large research attention owing to the usefulness of microalgae in bio-sequestration of CO2 from the emission source. In this study, one high CO2 tolerant (LAMB 31) and non-tolerant (LAMB 122) Chlorella sp. strains were transferred from air to 40% CO2, during which four time points were chosen for comparative transcriptome analysis. Gene changes started in the lag phase (T1) of population growth with more genes (7889) upregulated in LAMB 31 than in LAMB 122 (1092). Further function enrichments indicated: In LAMB 31, up-regulation of genes in cyclic electron transportation, F-type ATPase and Calvin cycle were associated with the enhancement of carbon fixation abilities; upregulation of genes in phosphorylation together with V-ATPase, which contributed to cytoplasmatic pH stability; Lastly, enhancement of carbon metabolisms including TCA cycle and glycolysis accelerated the consumption of cellular organic carbon. Most of the genes in these pathways and processes showed downregulation in LAMB 122. This study disclosed the most complete transcriptional molecular mechanisms of Chlorella sp. responding to high CO2 by combining CO2 fixation, transportation, and metabolic processes. The results provided valuable genetic information for future screening and breeding of microalgae with high-CO2 tolerance for more efficient CO2 bio-sequestration.
Collapse
Affiliation(s)
- Jun Li
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao 266003, China
| | - Kehou Pan
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266100, China; Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, No. 5 12 Yu Shan Road, Qingdao 266003, China
| | - Xuexi Tang
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
| | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, No. 5 12 Yu Shan Road, Qingdao 266003, China
| | - Baohua Zhu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, No. 5 12 Yu Shan Road, Qingdao 266003, China
| | - Yan Zhao
- College of Marine Life Sciences, Department of Marine Ecology, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
| |
Collapse
|
28
|
Slaveykova VI, Majumdar S, Regier N, Li W, Keller AA. Metabolomic Responses of Green Alga Chlamydomonas reinhardtii Exposed to Sublethal Concentrations of Inorganic and Methylmercury. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3876-3887. [PMID: 33631933 DOI: 10.1021/acs.est.0c08416] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Metabolomics characterizes low-molecular-weight molecules involved in different biochemical reactions and provides an integrated assessment of the physiological state of an organism. By using liquid chromatography-mass spectrometry targeted metabolomics, we examined the response of green alga Chlamydomonas reinhardtii to sublethal concentrations of inorganic mercury (IHg) and monomethylmercury (MeHg). We quantified the changes in the levels of 93 metabolites preselected based on the disturbed metabolic pathways obtained in a previous transcriptomics study. Metabolites are downstream products of the gene transcription; hence, metabolite quantification provided information about the biochemical status of the algal cells exposed to Hg compounds. The results showed that the alga adjusts its metabolism during 2 h exposure to 5 × 10-9 and 5 × 10-8 mol L-1 IHg and MeHg by increasing the level of various metabolites involved in amino acid and nucleotide metabolism, photorespiration, and tricarboxylic acid (TCA) cycle, as well as the metabolism of fatty acids, carbohydrates, and antioxidants. Most of the metabolic perturbations in the alga were common for IHg and MeHg treatments. However, the exposure to IHg resulted in more pronounced perturbations in the fatty acid and TCA metabolism as compared with the exposure to MeHg. The observed metabolic perturbations were generally consistent with our previously published transcriptomics results for C. reinhardtii exposed to the comparable level of IHg and MeHg. The results highlight the potential of metabolomics for toxicity evaluation, especially to detect effects at an early stage of exposure prior to their physiological appearance.
Collapse
Affiliation(s)
- Vera I Slaveykova
- Faculty of Sciences, Earth and Environment Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Environmental Biogeochemistry and Ecotoxicology, University of Geneva, Uni Carl Vogt, 66 Blvd Carl-Vogt, Geneva CH 1211, Switzerland
| | - Sanghamitra Majumdar
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, California 93106-5131, United States
| | - Nicole Regier
- Faculty of Sciences, Earth and Environment Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Environmental Biogeochemistry and Ecotoxicology, University of Geneva, Uni Carl Vogt, 66 Blvd Carl-Vogt, Geneva CH 1211, Switzerland
| | - Weiwei Li
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, California 93106-5131, United States
| | - Arturo A Keller
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, California 93106-5131, United States
| |
Collapse
|
29
|
Li N, Liu Y, Liang Z, Lou Y, Liu Y, Zhao X, Wang G. Influence of fuel oil on Platymonas helgolandica: An acute toxicity evaluation to amino acids. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 271:116226. [PMID: 33360349 DOI: 10.1016/j.envpol.2020.116226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
It is highly likely that the toxicity of water accommodated fractions (WAF) will influence marine microalgae, and consequently lead to potential risk for the marine ecological environment. However, it was often neglected whether WAF can influence the transformation of relative compounds in organisms. The metabolism of amino acids (AAs) can be used to track physiological changes in microalgae because amino acids are the basis of proteins and enzymes. In this study, using marine Chlorophyta Platymonas helgolandica as the test organism, the effects of different concentrations of WAF on AA compositions and stable carbon isotope ratios (δ13C) of individual AAs of Platymonas helgolandica were investigated. The results showed that the WAF of #180 fuel oil had an obvious suppressing effect on the growth and chlorophyll a content of microalgae. The growth inhibitory rate at 96 h was 80.66% at a WAF concentration of 0.50 mg L-1 compared with the control. Furthermore, seven among the 16 AAs, including alanine, cysteine, proline, aspartic acid, lysine, histidine and tyrosine, had relatively high abundance. Under the glycolysis pathway, the cysteine abundance was higher than control, meaning that the biosynthesized pathway of alanine through cysteine as a precursor could be damaged. Phosphoenolpyruvate (PEP) was an important synthesis precursor of alanine (leucine) and aromatic AA family (Phenylalanine and tyrosine), and played an important role in δ13CAAs fractionation under the WAF stress. Under the TCA pathway, to protect cell metabolism activities under WAF stress, the δ13C value of threonine and proline abundance in microalgae with the increase in WAF stress. Therefore, δ13CAAs fractionation can be used as a novel method for toxicity evaluation of WAF on future.
Collapse
Affiliation(s)
- Na Li
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Yu Liu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China; Environmental Information Institute, Dalian Maritime University, Dalian, China.
| | - Zhengyu Liang
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Yadi Lou
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Yuxin Liu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Xinda Zhao
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| | - Guoguang Wang
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, China
| |
Collapse
|
30
|
Revisiting nitrogen utilization in algae: A review on the process of regulation and assimilation. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.biteb.2020.100584] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
31
|
Metabolomics for early detection of stress in freshwater alga Poterioochromonas malhamensis exposed to silver nanoparticles. Sci Rep 2020; 10:20563. [PMID: 33239722 PMCID: PMC7689461 DOI: 10.1038/s41598-020-77521-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Silver nanoparticles (AgNPs) are one of the most used engineered nanomaterials. Despite progress in assessing their environmental implications, knowledge gaps exist concerning the metabolic perturbations induced by AgNPs on phytoplankton, essential organisms in global biogeochemical cycles and food-web dynamics. We combine targeted metabolomics, biouptake and physiological response studies to elucidate metabolic perturbations in alga Poterioochromonas malhamensis induced by AgNPs and dissolved Ag. We show time-dependent perturbation of the metabolism of amino acids, nucleotides, fatty acids, tricarboxylic acids, photosynthesis and photorespiration by both Ag-treatments. The results suggest that dissolved Ag ions released by AgNPs are the major toxicity driver; however, AgNPs internalized in food vacuoles contributed to the perturbation of amino acid metabolism, TCA cycle and oxidative stress. The metabolic perturbations corroborate the observed physiological responses. We highlight the potential of metabolomics as a tool for understanding the molecular basis for these metabolic and physiological changes, and for early detection of stress.
Collapse
|
32
|
Kuhlisch C, Althammer J, Sazhin AF, Jakobsen HH, Nejstgaard JC, Pohnert G. Metabolomics-derived marker metabolites to characterize Phaeocystis pouchetii physiology in natural plankton communities. Sci Rep 2020; 10:20444. [PMID: 33235278 PMCID: PMC7686483 DOI: 10.1038/s41598-020-77169-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 10/28/2020] [Indexed: 01/07/2023] Open
Abstract
Phaeocystis pouchetii (Hariot) Lagerheim, 1893 regularly dominates phytoplankton blooms in higher latitudes spanning from the English Channel to the Arctic. Through zooplankton grazing and microbial activity, it is considered to be a key resource for the entire marine food web, but the actual relevance of biomass transfer to higher trophic levels is still under discussion. Cell physiology and algal nutritional state are suggested to be major factors controlling the observed variability in zooplankton grazing. However, no data have so far yielded insights into the metabolic state of Phaeocystis populations that would allow testing this hypothesis. Therefore, endometabolic markers of different growth phases were determined in laboratory batch cultures using comparative metabolomics and quantified in different phytoplankton blooms in the field. Metabolites, produced during exponential, early and late stationary growth of P. pouchetii, were profiled using gas chromatography-mass spectrometry. Then, metabolites were characterized that correlate with the growth phases using multivariate statistical analysis. Free amino acids characterized the exponential growth, whereas the early stationary phase was correlated with sugar alcohols, mono- and disaccharides. In the late stationary phase, free fatty acids, sterols and terpenes increased. These marker metabolites were then traced in Phaeocystis blooms during a cruise in the Barents Sea and North Norwegian fjords. About 50 endometabolites of P. pouchetii were detected in natural phytoplankton communities. Mannitol, scyllo-inositol, 24-methylcholesta-5,22-dien-3β-ol, and several free fatty acids were characteristic for Phaeocystis-dominated blooms but showed variability between them. Distinct metabolic profiles were detected in the nutrient-depleted community in the inner Porsangerfjord (< 0.5 µM NO3-, < 0.1 µM PO 4 3- ), with high relative amounts of free mono- and disaccharides indicative for a limited culture. This study thereby shows how the variable physiology of phytoplankton can alter the metabolic landscape of entire plankton communities.
Collapse
Affiliation(s)
- Constanze Kuhlisch
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.,Department of Plant and Environmental Sciences, Weizmann Institute of Science, 234 Herzl Street, 7610001, Rehovot, Israel
| | - Julia Althammer
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.,JenaBios GmbH, Löbstedter Straße 80, 07749, Jena, Germany
| | - Andrey F Sazhin
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Nakhimovsky Prospect 36, Moscow, Russia
| | - Hans H Jakobsen
- Department of Bioscience, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Jens C Nejstgaard
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Dep. 3, Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstraße 8, 07743, Jena, Germany.
| |
Collapse
|
33
|
Thangaraj S, Sun J. Transcriptomic reprogramming of the oceanic diatom Skeletonema dohrnii under warming ocean and acidification. Environ Microbiol 2020; 23:980-995. [PMID: 32975013 DOI: 10.1111/1462-2920.15248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 12/19/2022]
Abstract
Under ocean warming and acidification, diatoms use a unique acclimation and adaptation strategy by saving energy and utilizing it for other cellular processes. However, the molecular mechanisms that underlie this reprogramming of energy utilization are currently unknown. Here, we investigate the metabolic reprogramming of the ecologically important diatom Skeletonema dohrnii grown under two different temperature (21°C and 25°C) and pCO2 (400 and 1000 ppm) levels, utilizing global transcriptomic analysis. We find that evolutionary changes in the baseline gene expression, which we termed transcriptional up- and downregulation, is the primary mechanism used by diatoms to acclimate to the combined conditions of ocean warming and acidification. This transcriptional regulation shows that under higher temperature and pCO2 conditions, photosynthesis, electron transport and carboxylation were modified with increasing abundances of genes encoding ATP, NADPH and carbon gaining for the carbon-dioxide-concentrating mechanisms (CCMs). Our results also indicate that changes in the transcriptional regulation of CCMs led to a decrease in the metabolic cost to save energy by promoting amino acid synthesis and nitrogen assimilation for the active protein processing machinery to adapt to warming and ocean acidification. This study generated unique metabolic insights into diatoms and suggests that future climate change conditions will cause evolutionary changes in oceanic diatoms that will facilitate their acclimation strategy.
Collapse
Affiliation(s)
- Satheeswaran Thangaraj
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, Hubei, 430074, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, Hubei, 430074, China
| |
Collapse
|
34
|
Co-Expression Networks for Causal Gene Identification Based on RNA-Seq Data of Corynebacterium pseudotuberculosis. Genes (Basel) 2020; 11:genes11070794. [PMID: 32674507 PMCID: PMC7397307 DOI: 10.3390/genes11070794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/19/2022] Open
Abstract
Corynebacterium pseudotuberculosis is a Gram-positive bacterium that causes caseous lymphadenitis, a disease that predominantly affects sheep, goat, cattle, buffalo, and horses, but has also been recognized in other animals. This bacterium generates a severe economic impact on countries producing meat. Gene expression studies using RNA-Seq are one of the most commonly used techniques to perform transcriptional experiments. Computational analysis of such data through reverse-engineering algorithms leads to a better understanding of the genome-wide complexity of gene interactomes, enabling the identification of genes having the most significant functions inferred by the activated stress response pathways. In this study, we identified the influential or causal genes from four RNA-Seq datasets from different stress conditions (high iron, low iron, acid, osmosis, and PH) in C. pseudotuberculosis, using a consensus-based network inference algorithm called miRsigand next identified the causal genes in the network using the miRinfluence tool, which is based on the influence diffusion model. We found that over 50% of the genes identified as influential had some essential cellular functions in the genomes. In the strains analyzed, most of the causal genes had crucial roles or participated in processes associated with the response to extracellular stresses, pathogenicity, membrane components, and essential genes. This research brings new insight into the understanding of virulence and infection by C. pseudotuberculosis.
Collapse
|
35
|
Seo S, Kim J, Lee JW, Nam O, Chang KS, Jin E. Enhanced pyruvate metabolism in plastids by overexpression of putative plastidial pyruvate transporter in Phaeodactylum tricornutum. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:120. [PMID: 32670407 PMCID: PMC7350735 DOI: 10.1186/s13068-020-01760-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 07/02/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The development of microalgal strains for enhanced biomass and biofuel production has received increased attention. Moreover, strain development via metabolic engineering for commercial production is being considered as the most efficient strategy. Pyruvate is an essential metabolite in the cells and plays an essential role in amino acid biosynthesis and de novo fatty acid biosynthesis in plastids. Although pyruvate can be a valuable target for metabolic engineering, its transporters have rarely been studied in microalgae. In this study, we aimed to identify the plastidial pyruvate transporter of Phaeodactylum tricornutum and utilize it for strain development. RESULTS We identified putative pyruvate transporter localized in the plastid membrane of Phaeodactylum tricornutum. Transformants overexpressing the pyruvate transporter were generated to increase the influx of pyruvate into plastids. Overexpression of a plastidial pyruvate transporter in P. tricornutum resulted in enhanced biomass (13.6% to 21.9%), lipid contents (11% to 30%), and growth (3.3% to 8.0%) compared to those of wild type during one-stage cultivation. CONCLUSION To regulate the pyruvate influx and its metabolism in plastids, we generated transformants overexpressing the putative plastidial pyruvate transporter in P. tricornutum. They showed that its overexpression for compartmentalizing pyruvate in plastids could be an attractive strategy for the effective production of biomass and lipids with better growth, via enhanced pyruvate metabolism in plastids.
Collapse
Affiliation(s)
- Seungbeom Seo
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - Joon Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - Jun-Woo Lee
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - Onyou Nam
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - Kwang Suk Chang
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul, 04763 Republic of Korea
| |
Collapse
|
36
|
The Biotechnological Potential of the Marine Diatom Skeletonema dohrnii to the Elevated Temperature and pCO 2 Concentration. Mar Drugs 2020; 18:md18050259. [PMID: 32429035 PMCID: PMC7281586 DOI: 10.3390/md18050259] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 11/17/2022] Open
Abstract
Marine diatoms are promising candidates for biotechnological applications, since they contain high-value compounds, naturally. To facilitate the production of these compounds, stress conditions are often preferable; however, challenges remain with respect to maximizing a metabolic potential for the large-scale cultivation. Here, we sequenced the transcriptome of diatom Skeletonema dohrnii under the actual (21 °C, 400 ppm) and elevated (25 °C, 1000 ppm) temperature and pCO2 condition. Results indicated that cells grown at higher temperature and pCO2 showed increasing growth rate, pigment composition, and biochemical productivity as did the expression of chlorophyll, carotenoid and bioactive compound related genes or transcripts. Furthermore, performing de novo transcriptome, we identified 32,884 transcript clusters and found 10,974 of them were differentially expressed between these two conditions. Analyzing the functions of differentially expressed transcripts, we found many of them involved in core metabolic and biosynthesis pathways, including chlorophyll metabolism, carotenoid, phenylpropanoid, phenylalanine and tyrosine, and flavonoid biosynthesis was upregulated. Moreover, we here demonstrated that utilizing a unique bio-fixation ability, S. dohrnii is capable of suppressing central carbon metabolism to promote lipid productivity, fatty acid contents and other bioactive compounds under high temperature and pCO2 treatment. Our study suggests that this S. dohrnii species could be a potential candidate for wide-scale biotechnological applications under elevated temperature and CO2 conditions.
Collapse
|
37
|
Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
Collapse
Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
| |
Collapse
|
38
|
Bjerkelund Røkke G, Hohmann-Marriott MF, Almaas E. An adjustable algal chloroplast plug-and-play model for genome-scale metabolic models. PLoS One 2020; 15:e0229408. [PMID: 32092117 PMCID: PMC7039451 DOI: 10.1371/journal.pone.0229408] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/05/2020] [Indexed: 01/25/2023] Open
Abstract
The chloroplast is a central part of plant cells, as this is the organelle where the photosynthesis, fixation of inorganic carbon, and other key functions related to fatty acid synthesis and amino acid synthesis occur. Since this organelle should be an integral part of any genome-scale metabolic model for a microalgae or a higher plant, it is of great interest to generate a detailed and standardized chloroplast model. Additionally, we see the need for a novel type of sub-model template, or organelle model, which could be incorporated into a larger, less specific genome-scale metabolic model, while allowing for minor differences between chloroplast-containing organisms. The result of this work is the very first standardized chloroplast model, iGR774, consisting of 788 reactions, 764 metabolites, and 774 genes. The model is currently able to run in three different modes, mimicking the chloroplast metabolism of three photosynthetic microalgae-Nannochloropsis gaditana, Chlamydomonas reinhardtii and Phaeodactylum tricornutum. In addition to developing the chloroplast metabolic network reconstruction, we have developed multiple software tools for working with this novel type of sub-model in the COBRA Toolbox for MATLAB, including tools for connecting the chloroplast model to a genome-scale metabolic reconstruction in need of a chloroplast, for switching the model between running in different organism modes, and for expanding it by introducing more reactions either related to one of the current organisms included in the model, or to a new organism.
Collapse
Affiliation(s)
- Gunvor Bjerkelund Røkke
- Department of Biotechnology and Food Science, The Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Eivind Almaas
- Department of Biotechnology and Food Science, The Norwegian University of Science and Technology, Trondheim, Norway
- K. G. Jebsen Center for Genetic Epidemiology, The Norwegian University of Science and Technology, Trondheim, Norway
| |
Collapse
|
39
|
Pan Y, Hu F, Yu C, Li C, Huang T, Hu H. Amino Acid Catabolism During Nitrogen Limitation in Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:589026. [PMID: 33408729 PMCID: PMC7780933 DOI: 10.3389/fpls.2020.589026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/23/2020] [Indexed: 05/08/2023]
Abstract
Diatoms can accumulate high levels of triacylglycerols (TAGs) under nitrogen depletion and have attracted increasing attention as a potential system for biofuel production. In Phaeodactylum tricornutum, a model diatom, about 40% of lipid is synthesized from the breakdown of cellular components under nitrogen starvation. Our previous studies indicated that carbon skeletons from enhanced branched-chain amino acid (BCAA) degradation under nitrogen deficiency contribute to TAG biosynthesis in P. tricornutum. In this review, we outlined the catabolic pathways of all 20 amino acids based on the genome, transcriptome, proteome, and metabolome data. The contribution of these amino acid catabolic pathways to TAG accumulation was also analyzed.
Collapse
Affiliation(s)
- Yufang Pan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Fan Hu
- School of Foreign Languages, China University of Geosciences, Wuhan, China
| | - Chen Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenjie Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Teng Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Hanhua Hu,
| |
Collapse
|
40
|
Ait-Mohamed O, Novák Vanclová AMG, Joli N, Liang Y, Zhao X, Genovesio A, Tirichine L, Bowler C, Dorrell RG. PhaeoNet: A Holistic RNAseq-Based Portrait of Transcriptional Coordination in the Model Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2020; 11:590949. [PMID: 33178253 PMCID: PMC7596299 DOI: 10.3389/fpls.2020.590949] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/15/2020] [Indexed: 05/04/2023]
Abstract
Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom Phaeodactylum tricornutum. Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the P. tricornutum genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in P. tricornutum chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.
Collapse
Affiliation(s)
- Ouardia Ait-Mohamed
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anna M. G. Novák Vanclová
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Nathalie Joli
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Yue Liang
- Department of Oceanography, Dalhousie University, Halifax, NS, Canada
| | - Xue Zhao
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
| | - Auguste Genovesio
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Leila Tirichine
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Université de Nantes, CNRS, UFIP, UMR 6286, Nantes, France
- *Correspondence: Leila Tirichine,
| | - Chris Bowler
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Chris Bowler,
| | - Richard G. Dorrell
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| |
Collapse
|
41
|
Ryu KH, Kim B, Heo S, Chang YK, Lee JH. Mathematical Modeling of Microalgal Internal Metabolic Behaviors under Heterotrophic Conditions and Its Application. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b05948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyung Hwan Ryu
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Boeun Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seongmin Heo
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yong-Keun Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- Advanced Biomass R&D Center, #2502 Building W1-3, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jay H. Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| |
Collapse
|
42
|
Zhu J, Yang Y, Duan S, Sun D. The Antialgal Mechanism of Luteolin-7-O-Glucuronide on Phaeocystis globosa by Metabolomics Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E3222. [PMID: 31484378 PMCID: PMC6747131 DOI: 10.3390/ijerph16173222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/01/2019] [Accepted: 09/02/2019] [Indexed: 11/22/2022]
Abstract
Antialgal compounds from plants have been identified as promising candidates for controlling harmful algal blooms (HABs). In our previous study, luteolin-7-O-glucuronide was used as a promising algistatic agent to control Phaeocystis globosa (P. globose) blooms; however, its antialgal mechanism on P. globosa have not yet been elaborated in detail. In this study, a liquid chromatography linked to tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomic approach was used to investigate changes in intracellular and extracellular metabolites of P. globosa after exposure to luteolin-7-O-glucuronide. Significant differences in intracellular metabolites profiles were observed between treated and untreated groups; nevertheless, metabolic statuses for extracellular metabolites were similar among these two groups. For intracellular metabolites, 20 identified metabolites showed significant difference. The contents of luteolin, gallic acid, betaine and three fatty acids were increased, while the contents of α-Ketoglutarate and acetyl-CoA involved in tricarboxylic acid cycle, glutamate, and 11 organic acids were decreased. Changes in those metabolites may be induced by the antialgal compound in response to stress. The results revealed that luteolin played a vital role in the antialgal mechanism of luteolin-7-O-glucuronide on P. globosa, because luteolin increased the most in the treatment groups and had strong antialgal activity on P. globosa. α-Ketoglutarate and acetyl-CoA were the most inhibited metabolites, indicating that the antialgal compound inhibited the growth through disturbed the tricarboxylic acid (TCA) cycle of algal cells. To summarize, our data provides insights into the antialgal mechanism of luteolin-7-O-glucuronide on P. globosa, which can be used to further control P. globosa blooms.
Collapse
Affiliation(s)
- Jingyi Zhu
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yeyin Yang
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Shunshan Duan
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Dong Sun
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| |
Collapse
|
43
|
Hano T, Tomaru Y. Metabolomics-based approach to explore growth phase-dependent markers in cultured diatom Chaetoceros tenuissimus. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1128:121779. [PMID: 31499295 DOI: 10.1016/j.jchromb.2019.121779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/17/2019] [Accepted: 08/26/2019] [Indexed: 01/21/2023]
Abstract
Chaetoceros tenuissimus is a cosmopolitan marine diatom whose metabolism has been little investigated. In this study, we examined the alterations of the metabolite profile between different growth phases (exponential and stationary phase) in cultured C. tenuissimus and identified growth phase-dependent candidate marker metabolite. First, the preparation methodology was optimized, focusing on extraction solvent. Metabolites of the cultured diatom (exponential phase 2.4 × 106 cells/mL, stationary phase 3.1 × 106 cells/mL) were extracted using two solvents with different constituents (solvent 1, methanol:H2O:chloroform = 5:2:2; solvent 2, methanol:ethanol:chloroform = 1:3:1). Gas chromatography mass spectrometry (GC/MS)-based metabolomics successfully detected 43 water-soluble metabolites in both solvents. The metabolic features were dependent on the growth phase: amino acid levels were higher in the exponential phase, whereas sugars and alcohols were more abundant in the stationary phase. Solvent 1 was superior in the recovery of the candidate metabolite that had a retention time of 18.13 min and predominantly contributed to discrimination between the growth phases; the metabolite level was higher in the stationary phase than in the exponential phase. The candidate metabolite was identified as mannonic acid by using GC/MS and liquid chromatography tandem mass spectrometry. Higher levels of mannonic acid during the stationary phase were also observed in other three diatom species. This study provides further insight into the use of metabolomics in the evaluation of physiological conditions of diatoms and suggests that mannonic acid content is a potential biomarker of the growth phase in cultured diatom cells.
Collapse
Affiliation(s)
- Takeshi Hano
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan. http://feis.fra.affrc.go.jp/
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| |
Collapse
|
44
|
Cirri E, De Decker S, Bilcke G, Werner M, Osuna-Cruz CM, De Veylder L, Vandepoele K, Werz O, Vyverman W, Pohnert G. Associated Bacteria Affect Sexual Reproduction by Altering Gene Expression and Metabolic Processes in a Biofilm Inhabiting Diatom. Front Microbiol 2019; 10:1790. [PMID: 31428077 PMCID: PMC6688387 DOI: 10.3389/fmicb.2019.01790] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/19/2019] [Indexed: 01/23/2023] Open
Abstract
Diatoms are unicellular algae with a fundamental role in global biogeochemical cycles as major primary producers at the base of aquatic food webs. In recent years, chemical communication between diatoms and associated bacteria has emerged as a key factor in diatom ecology, spurred by conceptual and technological advancements to study the mechanisms underlying these interactions. Here, we use a combination of physiological, transcriptomic, and metabolomic approaches to study the influence of naturally co-existing bacteria, Maribacter sp. and Roseovarius sp., on the sexual reproduction of the biofilm inhabiting marine pennate diatom Seminavis robusta. While Maribacter sp. severely reduces the reproductive success of S. robusta cultures, Roseovarius sp. slightly enhances it. Contrary to our expectation, we demonstrate that the effect of the bacterial exudates is not caused by altered cell-cycle regulation prior to the switch to meiosis. Instead, Maribacter sp. exudates cause a reduced production of diproline, the sexual attraction pheromone of S. robusta. Transcriptomic analyses show that this is likely an indirect consequence of altered intracellular metabolic fluxes in the diatom, especially those related to amino acid biosynthesis, oxidative stress response, and biosynthesis of defense molecules. This study provides the first insights into the influence of bacteria on diatom sexual reproduction and adds a new dimension to the complexity of a still understudied phenomenon in natural diatom populations.
Collapse
Affiliation(s)
- Emilio Cirri
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Sam De Decker
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Gust Bilcke
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Markus Werner
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
| | - Cristina Maria Osuna-Cruz
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wim Vyverman
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| |
Collapse
|
45
|
Metabolic Innovations Underpinning the Origin and Diversification of the Diatom Chloroplast. Biomolecules 2019; 9:biom9080322. [PMID: 31366180 PMCID: PMC6723447 DOI: 10.3390/biom9080322] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022] Open
Abstract
Of all the eukaryotic algal groups, diatoms make the most substantial contributions to photosynthesis in the contemporary ocean. Understanding the biological innovations that have occurred in the diatom chloroplast may provide us with explanations to the ecological success of this lineage and clues as to how best to exploit the biology of these organisms for biotechnology. In this paper, we use multi-species transcriptome datasets to compare chloroplast metabolism pathways in diatoms to other algal lineages. We identify possible diatom-specific innovations in chloroplast metabolism, including the completion of tocopherol synthesis via a chloroplast-targeted tocopherol cyclase, a complete chloroplast ornithine cycle, and chloroplast-targeted proteins involved in iron acquisition and CO2 concentration not shared between diatoms and their closest relatives in the stramenopiles. We additionally present a detailed investigation of the chloroplast metabolism of the oil-producing diatom Fistulifera solaris, which is of industrial interest for biofuel production. These include modified amino acid and pyruvate hub metabolism that might enhance acetyl-coA production for chloroplast lipid biosynthesis and the presence of a chloroplast-localised squalene synthesis pathway unknown in other diatoms. Our data provides valuable insights into the biological adaptations underpinning an ecologically critical lineage, and how chloroplast metabolism can change even at a species level in extant algae.
Collapse
|
46
|
Füssy Z, Faitová T, Oborník M. Subcellular Compartments Interplay for Carbon and Nitrogen Allocation in Chromera velia and Vitrella brassicaformis. Genome Biol Evol 2019; 11:1765-1779. [PMID: 31192348 PMCID: PMC6668581 DOI: 10.1093/gbe/evz123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Endosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol, and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in Chromera velia and Vitrella brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.
Collapse
Affiliation(s)
- Zoltán Füssy
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Tereza Faitová
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
- Faculty of Engineering and Natural Sciences, Department of Computer Science, Johannes Kepler University, Linz, Austria
| | - Miroslav Oborník
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| |
Collapse
|
47
|
L-tryptophan affects the essential oil of navel orange under various growing regions. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
48
|
Fernandes BS, Dias O, Costa G, Kaupert Neto AA, Resende TFC, Oliveira JVC, Riaño-Pachón DM, Zaiat M, Pradella JGC, Rocha I. Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production. BMC Biotechnol 2019; 19:41. [PMID: 31253157 PMCID: PMC6598237 DOI: 10.1186/s12896-019-0529-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/28/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pythium irregulare is an oleaginous Oomycete able to accumulate large amounts of lipids, including Eicosapentaenoic acid (EPA). EPA is an important and expensive dietary supplement with a promising and very competitive market, which is dependent on fish-oil extraction. This has prompted several research groups to study biotechnological routes to obtain specific fatty acids rather than a mixture of various lipids. Moreover, microorganisms can use low cost carbon sources for lipid production, thus reducing production costs. Previous studies have highlighted the production of EPA by P. irregulare, exploiting diverse low cost carbon sources that are produced in large amounts, such as vinasse, glycerol, and food wastewater. However, there is still a lack of knowledge about its biosynthetic pathways, because no functional annotation of any Pythium sp. exists yet. The goal of this work was to identify key genes and pathways related to EPA biosynthesis, in P. irregulare CBS 494.86, by sequencing and performing an unprecedented annotation of its genome, considering the possibility of using wastewater as a carbon source. RESULTS Genome sequencing provided 17,727 candidate genes, with 3809 of them associated with enzyme code and 945 with membrane transporter proteins. The functional annotation was compared with curated information of oleaginous organisms, understanding amino acids and fatty acids production, and consumption of carbon and nitrogen sources, present in the wastewater. The main features include the presence of genes related to the consumption of several sugars and candidate genes of unsaturated fatty acids production. CONCLUSIONS The whole metabolic genome presented, which is an unprecedented reconstruction of P. irregulare CBS 494.86, shows its potential to produce value-added products, in special EPA, for food and pharmaceutical industries, moreover it infers metabolic capabilities of the microorganism by incorporating information obtained from literature and genomic data, supplying information of great importance to future work.
Collapse
Affiliation(s)
- Bruna S Fernandes
- Department of Civil and Environmental Engineering, Federal University of Pernambuco, Recife, PE, Brazil.
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal.
| | - Oscar Dias
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Gisela Costa
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Antonio A Kaupert Neto
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Centre of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Tiago F C Resende
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal
| | - Juliana V C Oliveira
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Centre of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Diego M Riaño-Pachón
- Computational, Evolutionary and Systems Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Marcelo Zaiat
- Biological Processes Laboratory, Center for Research, Development and Innovation in Environmental Engineering, São Carlos School of Engineering (EESC), University of São Paulo, São Carlos, SP, Brazil.
| | | | - Isabel Rocha
- Centre of Biological Engineering, Universidade do Minho, Braga, Portugal.
| |
Collapse
|
49
|
Feltracco M, Barbaro E, Kirchgeorg T, Spolaor A, Turetta C, Zangrando R, Barbante C, Gambaro A. Free and combined L- and D-amino acids in Arctic aerosol. CHEMOSPHERE 2019; 220:412-421. [PMID: 30597360 DOI: 10.1016/j.chemosphere.2018.12.147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Aerosol samples were collected with a high-volume cascade impactor with a 10 day sampling frequency at the Gruvebadet observatory, close to Ny-Ålesund (Svalbard Islands). A total of 42 filters were analyzed for free and combined amino acids, as they are key components of bio-aerosol. This article provides the first investigation of free and combined L- and d-amino acids in Arctic atmospheric particulate matter. The main aim of this study was to determine how these compounds are distributed in size-segregated aerosols after short-range and long-range atmospheric transport and understand the possible sources of amino acids. The total load of free amino acids ranged from 2.0 to 10.8 pmol m-3, while combined amino acids ranged from 5.5 to 18.0 pmol m-3. At these levels amino compounds could play a role in the chemistry of cloud condensation nuclei and fine particles, for example by influencing their buffering capacity and basicity. Free and combined amino acids were mainly found in the fine aerosol fraction (<0.49 μm) and their concentrations could be affect by several sources, the most important of which were biological primary production and biomass burning.
Collapse
Affiliation(s)
- Matteo Feltracco
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy; Institute for the Dynamics of Environmental Processes CNR, Via Torino 155, 30172, Venice, Italy.
| | - Elena Barbaro
- Institute for the Dynamics of Environmental Processes CNR, Via Torino 155, 30172, Venice, Italy
| | - Torben Kirchgeorg
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy
| | - Andrea Spolaor
- Institute for the Dynamics of Environmental Processes CNR, Via Torino 155, 30172, Venice, Italy
| | - Clara Turetta
- Institute for the Dynamics of Environmental Processes CNR, Via Torino 155, 30172, Venice, Italy
| | - Roberta Zangrando
- Institute for the Dynamics of Environmental Processes CNR, Via Torino 155, 30172, Venice, Italy
| | - Carlo Barbante
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy; Institute for the Dynamics of Environmental Processes CNR, Via Torino 155, 30172, Venice, Italy
| | - Andrea Gambaro
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy; Institute for the Dynamics of Environmental Processes CNR, Via Torino 155, 30172, Venice, Italy
| |
Collapse
|
50
|
Ryu KH, Sung M, Kim B, Heo S, Chang YK, Lee JH. A mathematical model of intracellular behavior of microalgae for predicting growth and intracellular components syntheses under nutrient‐replete and ‐deplete conditions. Biotechnol Bioeng 2018; 115:2441-2455. [DOI: 10.1002/bit.26744] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/13/2018] [Accepted: 06/05/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Kyung Hwan Ryu
- Department of Chemical and Biomolecular EngineeringKorea Advanced Institute of Science and TechnologyDeajeon Republic of Korea
| | - Min‐Gyu Sung
- Department of Chemical and Biomolecular EngineeringKorea Advanced Institute of Science and TechnologyDeajeon Republic of Korea
| | - Boeun Kim
- Department of Chemical and Biomolecular EngineeringKorea Advanced Institute of Science and TechnologyDeajeon Republic of Korea
| | - Seongmin Heo
- Department of Chemical and Biomolecular EngineeringKorea Advanced Institute of Science and TechnologyDeajeon Republic of Korea
| | - Yong Keun Chang
- Department of Chemical and Biomolecular EngineeringKorea Advanced Institute of Science and TechnologyDeajeon Republic of Korea
- Advanced Biomass R&D Center, Korea Advanced Institute of Science and TechnologyDeajeon Republic of Korea
| | - Jay H. Lee
- Department of Chemical and Biomolecular EngineeringKorea Advanced Institute of Science and TechnologyDeajeon Republic of Korea
| |
Collapse
|