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Wang Y, Hu X, Sun Y, Wang C. Influence of the cold bottom water on taxonomic and functional composition and complexity of microbial communities in the southern Yellow Sea during the summer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143496. [PMID: 33248757 DOI: 10.1016/j.scitotenv.2020.143496] [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: 08/06/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 06/12/2023]
Abstract
The formation and presence of the cold bottom water (Yellow Sea Cold Water Mass, YSCWM) is a striking hydrological phenomenon in the southern Yellow Sea during the summer and has important effects on the marine ecosystem. To better understand its influence on microbial community structure and function, we compared the bacterial, archaeal and microeukaryotic communities in the cold water mass area (CWMA) and the southern area (SA) during the summer using amplicon and metagenomic sequencings. The habitat environment in the deep waters of the CWMA was characterized by higher salinity/DO/PO4-P, greater depth/distance to the coast, and lower levels of temperature/chlorophyll a/DIN/SiO3-Si/N:P ratio compared to that of the SA. Pure depth or distance to the coast explained a small portion of the microbial community variance, while environment explained a significant fraction of the variance when partialling the effects of depth and distance to the coast. Oligotrophic taxa (e.g. SAR11 clade Ia, Nitrosopumilus, Chloropicophyceae) dominated the deep water communities in the CWMA, while the common coastal taxa (e.g. Roseobacter strain HIMB11, Bacillariophyta, Noctilucophyceae) were more dominant in the deep waters of the SA, suggesting the great impact of the oligotrophic condition in the YSCWM on microbial communities. The microbial co-occurrence networks in the CWMA were less complex but contained a higher proportion of mutual exclusion relationship among prokaryotes; the prokaryotic α-diversity in the CWMA was significantly lower than in the SA while the microeukaryotic α-diversity was significantly higher in the CWMA, implying that prokaryotes and microeukaryotes respond to the cold water mass differently and the competition among prokaryotes was intensified under the impact of the YSCWM. Genes that relate to replication and repair accounted for a significantly lower proportion in the CWMA, which was likely an adaptation to the low carbon environment.
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Affiliation(s)
- Yibo Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Hu
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yanyu Sun
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caixia Wang
- Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Thangaraj S, Palanisamy SK, Zhang G, Sun J. Quantitative Proteomic Profiling of Marine Diatom Skeletonema dohrnii in Response to Temperature and Silicate Induced Environmental Stress. Front Microbiol 2021; 11:554832. [PMID: 33519723 PMCID: PMC7841394 DOI: 10.3389/fmicb.2020.554832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Global warming is expected to reduce the nutrient concentration in the upper ocean and affect the physiology of marine diatoms, but the underlying molecular mechanisms controlling these physiological changes are currently unknown. To understand these mechanisms, here we investigated iTRAQ based proteomic profiling of diatom Skeletonema dohrnii in a multifactorial experimental with a combining change of temperature and silicate concentrations. In total, 3369 differently abundant proteins were detected in four different environmental conditions, and the function of all proteins was identified using Gene Ontology and KEGG pathway analysis. For discriminating the proteome variation among samples, multivariate statistical analysis (PCA, PLS-DA) was performed by comparing the protein ratio differences. Further, performing pathway analysis on diatom proteomes, we here demonstrated downregulation of photosynthesis, carbon metabolism, and ribosome biogenesis in the cellular process that leads to decrease the oxidoreductase activity and affects the cell cycle of the diatom. Using PLS-DA VIP score plot analysis, we identified 15 protein biomarkers for discriminating studied samples. Of these, five proteins or gene (rbcL, PRK, atpB, DNA-binding, and signal transduction) identified as key biomarkers, induced by temperature and silicate stress in diatom metabolism. Our results show that proteomic finger-printing of S. dohrnii with different environmental conditions adds biological information that strengthens marine phytoplankton proteome analysis.
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Affiliation(s)
| | - Satheesh Kumar Palanisamy
- Department of Zoology, School of Natural Science, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Guicheng Zhang
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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León-Vaz A, Romero LC, Gotor C, León R, Vigara J. Effect of cadmium in the microalga Chlorella sorokiniana: A proteomic study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111301. [PMID: 32949933 DOI: 10.1016/j.ecoenv.2020.111301] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 06/11/2023]
Abstract
Cadmium is one of the most common heavy metals in contaminated aquatic environments and one of the most toxic contaminants for phytoplankton. Nevertheless, there are not enough studies focused on the effect of this metal in algae. Through a proteomic approach, this work shows how Cd can alter the growth, cell morphology and metabolism of the microalga Chlorella sorokiniana. Using the sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS), we concluded that exposure of Chlorella sorokiniana to 250 μM Cd2+ for 40 h caused downregulation of different metabolic pathways, such as photosynthesis, oxidative phosphorylation, glycolysis, TCA cycle and ribosomal proteins biosynthesis. However, photorespiration, antioxidant enzymes, gluconeogenesis, starch catabolism, and biosynthesis of glutamate, cysteine, glycine and serine were upregulated, under the same conditions. Finally, exposure to Cd also led to changes in the metabolism of carotenoids and lipids. In addition, the high tolerance of Chlorella sorokiniana to Cd points to this microalga as a potential microorganism to be used in bioremediation processes.
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Affiliation(s)
- Antonio León-Vaz
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 210071, Huelva, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49. 41092, Seville. Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Avenida Américo Vespucio, 49. 41092, Seville. Spain
| | - Rosa León
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 210071, Huelva, Spain
| | - Javier Vigara
- Laboratory of Biochemistry, Faculty of Experimental Sciences, Marine International Campus of Excellence and REMSMA, University of Huelva, 210071, Huelva, Spain.
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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.
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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
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Zhou B, Ma J, Chen F, Zou Y, Wei Y, Zhong H, Pan K. Mechanisms underlying silicon-dependent metal tolerance in the marine diatom Phaeodactylum tricornutum. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 262:114331. [PMID: 32443203 DOI: 10.1016/j.envpol.2020.114331] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic activities have significantly changed the stoichiometry and concentrations of nutrients in coastal waters. Silicon (Si) has become a potential limiting nutrient due to disproportionate nitrogen, phosphorus, and silicate inputs into these areas. The disrupted nutrient ratios can cause changes to metal sensitivity and accumulation in marine diatoms, an important group of eukaryotic phytoplankton that requires silicon for growth. In this study, we examined the effects of Si availability on the metal sensitivity in the diatom P. tricornutum. We found that Si starvation dramatically compromised its cadmium, copper, and lead tolerances. Interestingly, multiple lines of evidence indicated that Si-enriched cells had higher metal adsorption and influx rates than Si-starved cells. Yet Si-enriched cells also had a greater ability to respond to and counteract metal toxicity via elevated expression of membrane and vacuolar metal transporters and greater antioxidant activities which scavenge reactive oxygen species created by metal stress.
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Affiliation(s)
- Beibei Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jie Ma
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Fengyuan Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yue Zou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yang Wei
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Huan Zhong
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210046, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China.
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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.
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Thangaraj S, Giordano M, Sun J. Comparative Proteomic Analysis Reveals New Insights Into the Common and Specific Metabolic Regulation of the Diatom Skeletonema dohrnii to the Silicate and Temperature Availability. FRONTIERS IN PLANT SCIENCE 2020; 11:578915. [PMID: 33224167 PMCID: PMC7674209 DOI: 10.3389/fpls.2020.578915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/28/2020] [Indexed: 05/12/2023]
Abstract
Silicate (Si) and temperature are essential drivers for diatom growth and development in the ocean. Response of diatoms to these particular stress has been investigated; however, their common and specific responses to regulate intracellular development and growth are not known. Here, we investigated the combination of physiological characteristics and comparative proteomics of the diatom Skeletonema dohrnii grown in silicate- and temperature-limited conditions. Results show that cell carbon and lipid quotas were higher at lower-temperature cells, whereas cellular phosphate was higher in cells grown with lower Si. In silicate-limited cells, nitrate transporters were downregulated and resulted in lower nitrate assimilation, whereas the phosphate transporters and its assimilation were reduced in lower-temperature conditions. In photosynthesis, lower silicate caused impact in the linear electron flow and NADPH production, whereas cycling electron transport and ATP production were affected by the lower temperature. Concerning cell cycle, imbalances in the translation process were observed in lower-silicate cells, whereas impact in the transcription mechanism was observed in lower-temperature cells. However, proteins associated with carbon fixation and photorespiration were downregulated in both stress conditions, while the carbohydrate and lipid synthesis proteins were upregulated. Our results showed new insights into the common and specific responses on the proteome and physiology of S. dohrnii to silicate and temperature limitation, providing particular nutrient (Si)- and temperature-dependent mechanisms in diatoms.
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Affiliation(s)
- Satheeswaran Thangaraj
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences (Wuhan), Wuhan, China
- *Correspondence: Jun Sun,
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Protein and Proteome Atlas for Plants under Stresses: New Highlights and Ways for Integrated Omics in Post-Genomics Era. Int J Mol Sci 2019; 20:ijms20205222. [PMID: 31640274 PMCID: PMC6834174 DOI: 10.3390/ijms20205222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/02/2023] Open
Abstract
In the post-genomics era, integrative omics studies for biochemical, physiological, and molecular changes of plants in response to stress conditions play more crucial roles. Among them, atlas analysis of plants under different abiotic stresses, including salinity, drought, and toxic conditions, has become more important for uncovering the potential key genes and proteins in different plant tissues. High-quality genomic data and integrated analyses of transcriptomic, proteomic, metabolomics, and phenomic patterns provide a deeper understanding of how plants grow and survive under environmental stresses. This editorial mini-review aims to synthesize the 27 papers including two timely reviews that have contributed to this Special Issue, which focuses on concluding the recent progress in the Protein and Proteome Atlas in plants under different stresses. It covers various aspects of plant proteins ranging from agricultural proteomics, structure and function of proteins, novel techniques and approaches for gene and protein identification, protein quantification, proteomics for post-translational modifications (PTMs), and new insights into proteomics. The proteomics-based results in this issue will help the readers to gain novel insights for the understanding of complicated physiological processes in crops and other important plants in response to stressed conditions. Furthermore, these target genes and proteins that are important candidates for further functional validation in economic plants and crops can be studied.
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