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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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52
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Nieves-Morión M, Flores E, Foster RA. Predicting substrate exchange in marine diatom-heterocystous cyanobacteria symbioses. Environ Microbiol 2020; 22:2027-2052. [PMID: 32281201 DOI: 10.1111/1462-2920.15013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 11/27/2022]
Abstract
In the open ocean, some phytoplankton establish symbiosis with cyanobacteria. Some partnerships involve diatoms as hosts and heterocystous cyanobacteria as symbionts. Heterocysts are specialized cells for nitrogen fixation, and a function of the symbiotic cyanobacteria is to provide the host with nitrogen. However, both partners are photosynthetic and capable of carbon fixation, and the possible metabolites exchanged and mechanisms of transfer are poorly understood. The symbiont cellular location varies from internal to partial to fully external, and this is reflected in the symbiont genome size and content. In order to identify the membrane transporters potentially involved in metabolite exchange, we compare the draft genomes of three differently located symbionts with known transporters mainly from model free-living heterocystous cyanobacteria. The types and numbers of transporters are directly related to the symbiont cellular location: restricted in the endosymbionts and wider in the external symbiont. Three proposed models of metabolite exchange are suggested which take into account the type of transporters in the symbionts and the influence of their cellular location on the available nutrient pools. These models provide a basis for several hypotheses that given the importance of these symbioses in global N and C budgets, warrant future testing.
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Affiliation(s)
- Mercedes Nieves-Morión
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, Seville, E-41092, Spain
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
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Liu Q, Xing Y, Li Y, Wang H, Mi T, Zhen Y, Yu Z. Carbon fixation gene expression in Skeletonema marinoi in nitrogen-, phosphate-, silicate-starvation, and low-temperature stress exposure. JOURNAL OF PHYCOLOGY 2020; 56:310-323. [PMID: 31628865 DOI: 10.1111/jpy.12936] [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: 04/03/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Diatoms are unicellular algae with a set of extraordinary genes, metabolic pathways, and physiological functions acquired by secondary endosymbiosis, especially for their efficient photosynthetic carbon fixation mechanisms, which can be a reason for their successful environmental adaptation and great contribution to primary production. Based on the available genomic information, the expression patterns of carbon fixation genes were analyzed using transcriptomic sequencing and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in Skeletonema marinoi. Meanwhile, suitable reference genes applying to specific experimental treatments were selected. In our results, carbon fixation genes were standardized by actin and TATA box-binding protein-coding genes in growth phase samples and stress conditions, respectively. It was found that a series of carbon fixation genes, such as the pyruvate orthophosphate dikinase (PPDK)-coding gene, had significantly up-regulated expression in nitrogen-starvation, phosphate-starvation, and low-temperature conditions, but consistently down-regulated in silicate-starvation treatment. These carbon fixation genes exhibited variable expression levels in different conditions and will be useful for investigating gene expression mechanisms in S. marinoi and improve our understanding of diatom carbon fixation pathways.
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Affiliation(s)
- Qian Liu
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Yongze Xing
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Sciences Academy, Beihai, 536000, China
| | - Ying Li
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Hualong Wang
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Tiezhu Mi
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Yu Zhen
- Key laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, 266100, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao, 266100, China
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54
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Shiny Matilda C, Madhusudan I, Gaurav Isola R, Shanthi C. Potential of proteomics to probe microbes. J Basic Microbiol 2020; 60:471-483. [PMID: 32212201 DOI: 10.1002/jobm.201900628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 01/05/2023]
Abstract
An organism exposed to a plethora of environmental perturbations undergoes proteomic changes which enable the characterization of total proteins in it. Much of the proteomic information is obtained from genomic data. Additional information on the proteome such as posttranslational modifications, protein-protein interactions, protein localization, metabolic pathways, and so on are deduced using proteomic tools which genomics and transcriptomics fail to offer. The proteomic analysis allows identification of precise changes in proteins, which in turn solve the complexity of microbial population providing insights into the microbial metabolism, cellular pathways, and behavior of microorganisms in new environments. Furthermore, they provide clues for the exploitation of their special features for biotechnological applications. Numerous techniques for the analysis of microbial proteome such as electrophoretic, chromatographic, mass spectrometric-based methods as well as quantitative proteomics are available which facilitate protein separation, expression, identification, and quantification of proteins. An understanding of the potential of each of the proteomic tools has created a significant impact on diverse microbiological aspects and the same has been discussed in this review.
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Affiliation(s)
- Chellaiah Shiny Matilda
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Iyengar Madhusudan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Ravi Gaurav Isola
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
| | - Chittibabu Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
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55
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Kumar Sharma A, Mühlroth A, Jouhet J, Maréchal E, Alipanah L, Kissen R, Brembu T, Bones AM, Winge P. The Myb-like transcription factor phosphorus starvation response (PtPSR) controls conditional P acquisition and remodelling in marine microalgae. THE NEW PHYTOLOGIST 2020; 225:2380-2395. [PMID: 31598973 DOI: 10.1111/nph.16248] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/29/2019] [Indexed: 05/10/2023]
Abstract
Phosphorus (P) is one of the limiting macronutrients for algal growth in marine environments. Microalgae have developed adaptation mechanisms to P limitation that involve remodelling of internal phosphate resources and accumulation of lipids. Here, we used in silico analyses to identify the P-stress regulator PtPSR (Phaeodactylum tricornutum phosphorus starvation response) in the diatom P. tricornutum. ptpsr mutant lines were generated using gene editing and characterised by various molecular, genetics and biochemical tools. PtPSR belongs to a clade of Myb transcription factors that are conserved in stramenopiles and distantly related to plant P-stress regulators. PtPSR bound specifically to a conserved cis-regulatory element found in the regulatory region of P-stress-induced genes. ptpsr knockout mutants showed reduction in cell growth under P limitation. P-stress responses were impaired in ptpsr mutants compared with wild-type, including reduced induction of P-stress response genes, near to complete loss of alkaline phosphatase activity and reduced phospholipid degradation. We conclude that PtPSR is a key transcription factor influencing P scavenging, phospholipid remodelling and cell growth in adaptation to P stress in diatoms.
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Affiliation(s)
- Amit Kumar Sharma
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Alice Mühlroth
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, 38000, Grenoble, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, 38000, Grenoble, France
| | - Leila Alipanah
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Ralph Kissen
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Tore Brembu
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
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56
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Alexander H, Rouco M, Haley ST, Dyhrman ST. Transcriptional response of
Emiliania huxleyi
under changing nutrient environments in the North Pacific Subtropical Gyre. Environ Microbiol 2020; 22:1847-1860. [DOI: 10.1111/1462-2920.14942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Harriet Alexander
- Biology Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Mónica Rouco
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
- Department of Earth and Environmental Sciences Columbia University Palisades NY 10964 USA
| | - Sheean T. Haley
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
| | - Sonya T. Dyhrman
- Biology and Paleo Environment Division, Lamont‐Doherty Earth Observatory Columbia University Palisades NY 10964 USA
- Department of Earth and Environmental Sciences Columbia University Palisades NY 10964 USA
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57
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Zhang X, Lin S, Liu D. Transcriptomic and physiological responses of Skeletonema costatum to ATP utilization. Environ Microbiol 2020; 22:1861-1869. [PMID: 32077205 DOI: 10.1111/1462-2920.14944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 11/26/2022]
Abstract
The capacity of phytoplankton to utilize dissolved organic phosphorus (DOP) plays an important role in their competition for resources when the availability of dissolved inorganic phosphorus (DIP) is low in the aquatic systems. Here, we explored the physiological and molecular responses of a globally distributed marine diatom, Skeletonema costatum, in utilizing adenosine-5'-triphosphate (ATP) based on incubation experiments under ATP, DIP-replete, and DIP-depleted conditions. The results show that ATP supports the growth of S. costatum as efficiently as DIP. The pathway of S. costatum involved in utilizing ATP is not related to alkaline phosphatase (AP), an important DOP hydrolase, although extracellular hydrolysis is involved. The transcriptome analysis revealed several transcripts related to the hydrolase activity (e.g. NAD+ diphosphatase), which were significantly upregulated in the ATP culture group, indicating their possible involvement in ATP hydrolysis. Meanwhile, ATP-grown S. costatum exhibited downregulation of the genes related to a series of metabolic activities (e.g. purine metabolism), apparently to adapt to ATP condition.
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Affiliation(s)
- Xiaohua Zhang
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Department of Gene Engineering, Binzhou Medical University, Yantai, 264003, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA
| | - Dongyan Liu
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200241, China
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58
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Ou L, Qin X, Shi X, Feng Q, Zhang S, Lu S, Qi Y. Alkaline phosphatase activities and regulation in three harmful Prorocentrum species from the coastal waters of the East China Sea. MICROBIAL ECOLOGY 2020; 79:459-471. [PMID: 31267157 DOI: 10.1007/s00248-019-01399-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 06/07/2019] [Indexed: 06/09/2023]
Abstract
Harmful blooms of Prorocentrum donghaiense occur annually in the phosphorus-scarce coastal waters of the East China Sea (ECS). The enzymatic activities of alkaline phosphatase (AP) and its regulation by external phosphorus were studied during a P. donghaiense bloom in this area. The AP characteristics of P. donghaiense was further compared with Prorocentrum minimum and Prorocentrum micans in monocultures with both bulk and single-cell enzyme-labeled fluorescence AP assays. Concentrations of dissolved inorganic phosphorus (DIP) varied between 0.04 and 0.73 μmol l-1, with more than half recording stations registering concentrations below 0.10 μmol l-1. Concentrations of dissolved organic phosphorus (DOP) were comparable or even higher than those of DIP. P. donghaiense suffered phosphorus stress and expressed abundant AP, especially when DIP was lower than 0.10 μmol l-1. The AP activities showed a negative correlation with DIP but a positive correlation with DOP. The AP activities were also regulated by internal phosphorus pool. The sharp increase in AP activities was observed until cellular phosphorus was exhausted. Most AP of P. donghaiense was located on the cell surface and some were released into the water with time. Compared with P. minimum and P. micans, P. donghaiense showed a higher AP affinity for organic phosphorus substrates, a more efficient and energy-saving AP expression quantity as a response to phosphorus deficiency. The unique AP characteristic of P. donghaiense suggests that it benefits from the efficient utilization of DOP, and outcompete other species in the phosphorus-scarce ECS.
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Affiliation(s)
- Linjian Ou
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China.
| | - Xianling Qin
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China
- Guangxi Key Laboratory of Marine Environmental Science, and Guangxi Academy of Sciences, Nanning, 530007, People's Republic of China
| | - Xiaoyong Shi
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266100, People's Republic of China
- National Marine Hazard Mitigation Service, Beijing, 100194, People's Republic of China
| | - Qingliang Feng
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Shuwen Zhang
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Songhui Lu
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China.
| | - Yuzao Qi
- Research Center of Harmful Algae and Marine Biology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, 510632, People's Republic of China
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59
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Peng Q, Fang X, Zong X, He Q, Zhu T, Han S, Li S. Comparative transcriptome analysis of Bambusa pervariabilis × Dendrocalamopsis grandis against Arthrinium phaeospermum under protein AP-toxin induction. Gene 2020; 725:144160. [PMID: 31639431 DOI: 10.1016/j.gene.2019.144160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/05/2019] [Accepted: 10/07/2019] [Indexed: 01/01/2023]
Abstract
Bambusapervariabilis × Dendrocalamopsisgrandis, a fast-growing and easily propagated bamboo species, has been extensively planted in the southern China, resulting in huge ecological benefits. In recent years, it was found that the pathogenic fungus Arthrinium phaeospermum caused the death of a large amount of bamboo. In this study, the transcriptome of B. pervariabilis × D. grandis, induced by inactivated protein AP-toxin from A. phaeospermum was sequenced and analyzed, to reveal the resistance mechanism induced by biotic agents of B. pervariabilis × D. grandis against A. phaeospermum at the gene level. Transcriptome sequencing was performed by Illumina HiSeq 2000 in order to analyze the differentially expressed genes (DEGs) of B. pervariabilis × D. grandis in response to different treatment conditions. In total, 201,875,606 clean reads were obtained, and the percentage of Q30 bases in each sample was more than 94.21%. There were 6398 DEGs in the D-J group (inoculation with a pathogenic spore suspension after three days of AP-toxin induction) compared to the S-J group (inoculation with a pathogenic spore suspension after inoculation of sterile water for three days) with 3297 up-regulated and 3101 down-regulated genes. For the D-S group (inoculation with sterile water after inoculation of AP-toxin for three days), there were 2032 DEGs in comparison to the S-S group (inoculation with sterile water only), with 1035 up-regulated genes and 997 down-regulated genes. These identified genes were mainly involved in lignin and phytoprotein synthesis, tetrapyrrole synthesis, redox reactions, photosynthesis, and other processes. The fluorescence quantitative results showed that 22 pairs of primer amplification products were up-regulated and 7 were down-regulated. The rate of similarity between these results and the sequencing results of the transcription group was 100%, which confirmed the authenticity of the transcriptome sequencing results. Redox proteins, phenylalanine ammonia lyase, and S-adenosine-L-methionine synthetase, among others, were highly expressed; these results may indicate the level of disease resistance of the bamboo. These results provide a foundation for the further exploration of resistance genes and their functions.
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Affiliation(s)
- Qi Peng
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, Sichuan Province, China
| | - Xinmei Fang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, Sichuan Province, China
| | - Xiaozhuo Zong
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, Sichuan Province, China
| | - Qianqian He
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, Sichuan Province, China
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, Sichuan Province, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, Sichuan Province, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, Sichuan Province, China.
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60
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Wang H, Chen F, Mi T, Liu Q, Yu Z, Zhen Y. Responses of Marine Diatom Skeletonema marinoi to Nutrient Deficiency: Programmed Cell Death. Appl Environ Microbiol 2020; 86:e02460-19. [PMID: 31757826 PMCID: PMC6974647 DOI: 10.1128/aem.02460-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/15/2019] [Indexed: 11/20/2022] Open
Abstract
Diatoms are important phytoplankton and contribute greatly to the primary productivity of marine ecosystems. Despite the ecological significance of diatoms and the importance of programmed cell death (PCD) in the fluctuation of diatom populations, little is known about the molecular mechanisms of PCD triggered by different nutrient stresses. Here we describe the physiological, morphological, biochemical, and molecular changes in response to low levels of nutrients in the ubiquitous diatom Skeletonema marinoi The levels of gene expression involved in oxidation resistance and PCD strongly increased upon nitrogen (N) or phosphorus (P) starvation. The enzymatic activity of caspase 3-like protein also increased. Differences in mRNA levels and protein activities were observed between the low-N and low-P treatments, suggesting that PCD could have a differential response to different nutrient stresses. When cultures were replete with N or P, the growth inhibition stopped. Meanwhile, the enzymatic activity of caspase 3-like protein and the number of cells with damaged membranes decreased. These results suggest that PCD is an important cell fate decision mechanism in the marine diatom S. marinoi Our results provide important insight into how diatoms adjust phenotypic and genotypic features of their cell-regulated death programs when stressed by nutrient limitations. Overall, this study could allow us to better understand the molecular mechanism behind the formation and termination of diatom blooms in the marine environment.IMPORTANCE Our study showed how the ubiquitous diatom S. marinoi responded to different nutrient limitations with PCD in terms of physiological, morphological, biochemical, and molecular characteristics. Some PCD-related genes (PDCD4, GOX, and HSP90) induced by N deficiency were relatively upregulated compared to those induced by P deficiency. In contrast, the expression of the TSG101 gene in S. marinoi showed a clear and constant increase during P limitation compared to N limitation. These findings suggest that PCD is a complex mechanism involving several different proteins. The systematic mRNA level investigations provide new insight into understanding the oxidative stress- and cell death-related functional genes of diatoms involved in the response to nutrient fluctuations (N or P stress) in the marine environment.
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Affiliation(s)
- Hualong Wang
- College of Marine Life Science, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Tiezhu Mi
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Qian Liu
- College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao, China
| | - Yu Zhen
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
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61
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Snow JT, Holdship P, Rickaby REM. Antagonistic co-limitation through ion promiscuity - On the metal sensitivity of Thalassiosira oceanica under phosphorus stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 699:134080. [PMID: 31677461 DOI: 10.1016/j.scitotenv.2019.134080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/08/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Nutrient limitation of primary producers is a fundamental principle in biogeochemical oceanography and has been used with great success in prescribing understanding to patterns of marine primary productivity. In recent years the paradigm of nutrient limitation has expanded from single nutrient limitation towards concepts of co-limitation by multiple resources. Interactive effects between multiple limiting resources are now thought commonplace in marine microbial communities. Here we investigate the response exhibited by phosphate-limited Thalassiosira oceanica to elevated concentrations of the phosphate analogs vanadate, arsenate and molybdate. Enrichments in external arsenate and vanadate to phosphate-limited cultures act to suppress growth rates entirely, an effect not seen in phosphate replete conditions. Retardation of growth rates is attributed to mistaken uptake through ion promiscuity as evidenced by observations of significant intracellular accumulation of both arsenic and vanadium under phosphate limited conditions. We describe this novel co-limitation scenario as dependent antagonistic co-limitation (DAC), and suggest that this phenomenon of non-deliberate intracellular accumulation could be used as both a proxy of phosphate stress in the modern ocean and a possible marker of phosphate depletion limiting the duration of oceanic anoxic events.
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Affiliation(s)
- Joseph T Snow
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
| | - Philip Holdship
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Rosalind E M Rickaby
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
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62
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Hennon GMM, Dyhrman ST. Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms. HARMFUL ALGAE 2020; 91:101587. [PMID: 32057337 DOI: 10.1016/j.hal.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/10/2023]
Abstract
Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.
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Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.
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63
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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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Li J, Plouchart D, Zastepa A, Dittrich M. Picoplankton accumulate and recycle polyphosphate to support high primary productivity in coastal Lake Ontario. Sci Rep 2019; 9:19563. [PMID: 31862973 PMCID: PMC6925121 DOI: 10.1038/s41598-019-56042-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/03/2019] [Indexed: 11/08/2022] Open
Abstract
Phytoplankton can accumulate polyphosphate (polyP) to alleviate limitation of essential nutrient phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle remain elusive. Previously reported polyP enrichment in low-phosphorus oligotrophic marine waters contradicts the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic bay of Lake Ontario, planktonic polyP is controlled by multiple mechanisms and responds strongly to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under acute P stress. Low phosphorus also triggers enrichment of polyP that can be preferentially recycled to attenuate P lost. We discover that picoplankton, despite their low production rates, are responsible for the dynamic polyP metabolisms. Picoplankton store and liberate polyP to support the high primary productivity of blooming algae. PolyP mechanisms enable efficient P recycling on ecosystem and even larger scales.
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Affiliation(s)
- Jiying Li
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada.
| | - Diane Plouchart
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
| | - Arthur Zastepa
- Canada Center for Inland Waters, Environment and Climate Change Canada, Burlington, ON, L7S 1A1, Canada
| | - Maria Dittrich
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C 1A4, Canada
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Zhang SF, Yuan CJ, Chen Y, Lin L, Wang DZ. Transcriptomic response to changing ambient phosphorus in the marine dinoflagellate Prorocentrum donghaiense. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:1037-1047. [PMID: 31539936 DOI: 10.1016/j.scitotenv.2019.07.291] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/15/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
Dinoflagellates represent major contributors to the harmful algal blooms in the oceans. Phosphorus (P) is an essential macronutrient that limits the growth and proliferation of dinoflagellates. However, the specific molecular mechanisms involved in the P acclimation of dinoflagellates remain poorly understood. Here, the transcriptomes of a dinoflagellate Prorocentrum donghaiense grown under inorganic P-replete, P-deficient, and inorganic- and organic P-resupplied conditions were compared. Genes encoding low- and high-affinity P transporters were significantly down-regulated in the P-deficient cells, while organic P utilization genes were significantly up-regulated, indicating strong ability of P. donghaiense to utilize organic P. Up-regulation of membrane phospholipid catabolism and endocytosis provided intracellular and extracellular organic P for the P-deficient cells. Physiological responses of P. donghaiense to dissolved inorganic P (DIP) or dissolved organic P (DOP) resupply exhibited insignificant differences. However, the corresponding transcriptomic responses significantly differed. Although the expression of multiple genes was significantly altered after DIP resupplementation, few biological processes varied. In contrast, various metabolic processes associated with cell growth, such as translation, transport, nucleotide, carbohydrate and lipid metabolisms, were significantly altered in the DOP-resupplied cells. Our results indicated that P. donghaiense evolved diverse DOP utilization strategies to adapt to low P environments, and that DOPs might play critical roles in the P. donghaiense bloom formation.
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Affiliation(s)
- Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Chun-Juan Yuan
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Ying Chen
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen 361102, China; Key Laboratory of Marine Ecology & Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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Tian-Tian L, Ping H, Jia-Xing L, Zhi-Xin K, Ye-Hui T. Utilization of different dissolved organic phosphorus sources by Symbiodinium voratum in vitro. FEMS Microbiol Ecol 2019; 95:fiz150. [PMID: 31580458 DOI: 10.1093/femsec/fiz150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/02/2019] [Indexed: 11/14/2022] Open
Abstract
This study examines the physiological responses of the Symbiodiniumvoratum (clade E) to two types of phosphates having different chemical bonds-phosphoesters (C-O-P bonds) and phosphonates (C-P bonds) to explore Symbiodinium cell growth and the molecular perspective of the P utilization process. Alkaline phosphatase (AP), PhnX, PhoA and PhoX expression was profiled for different P conditions using the RT-qPCR method. In a sterile system, Symbiodinium could decompose phosphoesters, such as ATP and glucose 6-phosphate (G-6-P), into dissolved inorganic P (DIP) to supplement inorganic phosphorus but could not directly use phosphoesters for growth. The growth rate and photosynthetic efficiency of zooxanthellae in phosphoester-containing media did not significantly differ from those in the DIP group but were significantly inhibited in medium containing phosphonates such as N-(phosphonomethyl)glycine (glyphosate) and 2-aminoethylphosphonic acid (2-AEP), as well as in DIP-poor medium. The phosphonate group DIP concentration did not change remarkably, indicating that phosphonates can neither be directly used by zooxanthellae nor decomposed into DIP. Our RT-qPCR results support our views that the phosphoesters (C-O-P) had been hydrolyzed outside the cell before being absorbed into the Symbiodinium cell, and implies that PhnX, PhoA and PhoX are perhaps responsible for transporting DIP from medium into cells and for storage of DIP.
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Affiliation(s)
- Liu Tian-Tian
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences (ISEE, CAS)
| | - Huang Ping
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Liu Jia-Xing
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences (ISEE, CAS)
| | - Ke Zhi-Xin
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences (ISEE, CAS)
| | - Tan Ye-Hui
- Key Laboratory of Tropical Marine Bio-resources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology (LAMB), Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences (ISEE, CAS)
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Kang LK, Rynearson TA. Identification and Expression Analyses of the Nitrate Transporter Gene (NRT2) Family Among Skeletonema species (Bacillariophyceae). JOURNAL OF PHYCOLOGY 2019; 55:1115-1125. [PMID: 31233616 DOI: 10.1111/jpy.12896] [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: 07/31/2018] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
High-affinity nitrate transporters are considered to be the major transporter system for nitrate uptake in diatoms. In the diatom genus Skeletonema, three forms of genes encoding high-affinity nitrate transporters (NRT2) were newly identified from transcriptomes generated as part of the marine microbial eukaryote transcriptome sequencing project. To examine the expression of each form of NRT2 under different nitrogen environments, laboratory experiments were conducted under nitrate-sufficient, ammonium-sufficient, and nitrate-limited conditions using three ecologically important Skeletonema species: S. dohrnii, S. menzelii, and S. marinoi. Primers were developed for each NRT2 form and species and Q-RT-PCR was performed. For each NRT2 form, the three Skeletonema species had similar transcriptional patterns. The transcript levels of NRT2:1 were significantly elevated under nitrogen-limited conditions, but strongly repressed in the presence of ammonium. The transcript levels of NRT2:2 were also repressed by ammonium, but increased 5- to 10-fold under nitrate-sufficient and nitrogen-limited conditions. Finally, the transcript levels of NRT2:3 did not vary significantly under various nitrogen conditions, and behaved more like a constitutively expressed gene. Based on the observed transcript variation among NRT2 forms, we propose a revised model describing nitrate uptake kinetics regulated by multiple forms of nitrate transporter genes in response to various nitrogen conditions in Skeletonema. The differential NRT2 transcriptional responses among species suggest that species-specific adaptive strategies exist within this genus to cope with environmental changes.
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Affiliation(s)
- Lee-Kuo Kang
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, 20224, Taiwan
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Tatiana A Rynearson
- Graduate School of Oceanography, University of Rhode Island, Narragansett, Rhode Island, 02882, USA
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68
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Zhang H, He YB, Wu PF, Zhang SF, Xie ZX, Li DX, Lin L, Chen F, Wang DZ. Functional Differences in the Blooming Phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense Revealed by Comparative Metaproteomics. Appl Environ Microbiol 2019; 85:e01425-19. [PMID: 31375486 PMCID: PMC6752027 DOI: 10.1128/aem.01425-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/07/2019] [Indexed: 12/21/2022] Open
Abstract
Phytoplankton blooms are natural phenomena in the ocean, which are the results of rapid cell growth of some phytoplankton species in a unique environment. However, little is known about the molecular events occurring during the bloom. Here, we compared metaproteomes of two phytoplankton Heterosigma akashiwo and Prorocentrum donghaiense in the coastal East China Sea. H. akashiwo and P. donghaiense accounted for 7.82% and 4.74% of the phytoplankton community protein abundances in the nonbloom sample, whereas they contributed to 60.13% and 78.09%, respectively, in their individual blooming samples. Compared with P. donghaiense, H. akashiwo possessed a significantly higher abundance of light-harvesting complex proteins, carbonic anhydrasem and RuBisCO. The blooming H. akashiwo cells expressed more proteins related to external nutrient acquisition, such as bicarbonate transporter SLC4, ammonium transporter, nitrite transporter, and alkaline phosphatase, while the blooming P. donghaiense cells highly expressed proteins related to extra- and intracellular organic nutrient utilization, such as amino acid transporter, 5'-nucleotidase, acid phosphatase, and tripeptidyl-peptidase. The strong capabilities of light harvesting, as well as acquisition and assimilation of inorganic carbon, nitrogen, and phosphorus, facilitated the formation of the H. akashiwo bloom under the high turbidity and inorganic nutrient-sufficient condition, whereas the competitive advantages in organic nutrient acquisition and reallocation guaranteed the occurrence of the P. donghaiense bloom under the inorganic nutrient-insufficient condition. This study highlights the power of metaproteomics for revealing the underlying molecular behaviors of different coexisting phytoplankton species and advances our knowledge on the formation of phytoplankton blooms.IMPORTANCE A deep understanding of the mechanisms driving bloom formation is a prerequisite for effective bloom management. Metaproteomics was applied in this study to reveal the adaptive and responsive strategies of two coexisting phytoplankton species, H. akashiwo and P. donghaiense, during their bloom periods. Metabolic features and niche divergence in light harvesting, as well as carbon, nitrogen, and phosphorus acquisition and assimilation likely promoted the bloom occurrence under different environments. The molecular behaviors of coexisting bloom-causing species will give clues for bloom monitoring and management in the oceans.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yan-Bin He
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Peng-Fei Wu
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dong-Xu Li
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
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Liang J, Iqbal S, Wen F, Tong M, Liu J. Phosphorus-Induced Lipid Class Alteration Revealed by Lipidomic and Transcriptomic Profiling in Oleaginous Microalga Nannochloropsis sp. PJ12. Mar Drugs 2019; 17:md17090519. [PMID: 31484443 PMCID: PMC6780086 DOI: 10.3390/md17090519] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 12/22/2022] Open
Abstract
Phytoplankton are primary producers in the marine ecosystem, where phosphorus is often a limiting factor of their growth. Hence, they have evolved strategies to recycle phosphorus by replacing membrane phospholipids with phosphorus-free lipids. However, mechanisms for replacement of lipid classes remain poorly understood. To improve our understanding, we performed the lipidomic and transcriptomic profiling analyses of an oleaginous marine microalga Nannochloropsis sp. PJ12 in response to phosphorus depletion (PD) and replenishing. In this study, by using (liquid chromatography couple with tandem mass spectrometry) LC-MS/MS-based lipidomic analysis, we show that membrane phospholipid levels are significantly reduced upon PD, while phosphorus-free betaine lipid levels are increased. However, levels of phosphorus-free photosynthetic galactolipid and sulfolipid are not increased upon PD, consistent with the reduced photosynthetic activity. RNA-seq-based transcriptomic analysis indicates that enzymes involved in phospholipid recycling and phosphorus-free lipid synthesis are upregulated, supporting the lipidomic analysis. Furthermore, enzymes involved in FASII (type II fatty acid synthesis) elongation cycle upon PD are transcriptionally downregulated. EPA (eicosapentaenoic acid) level decrease upon PD is revealed by both GC-MS (gas chromatography coupled with mass spectrometry) and LC-MS/MS-based lipidomic analyses. PD-induced alteration is reversed after phosphorus replenishing. Taken together, our results suggest that the alteration of lipid classes upon environmental change of phosphorus is a result of remodeling rather than de novo synthesis in Nannochloropsis sp. PJ12.
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Affiliation(s)
- Jibei Liang
- Ocean College, Zhejiang University, Zhoushan 316000, China.
- School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China.
| | - Sunya Iqbal
- Ocean College, Zhejiang University, Zhoushan 316000, China.
| | - Fang Wen
- Ocean College, Zhejiang University, Zhoushan 316000, China.
| | - Mengmeng Tong
- Ocean College, Zhejiang University, Zhoushan 316000, China.
| | - Jianhua Liu
- School of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China.
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Non-Conventional Metal Ion Cofactor Requirement of Dinoflagellate Alkaline Phosphatase and Translational Regulation by Phosphorus Limitation. Microorganisms 2019; 7:microorganisms7080232. [PMID: 31374942 PMCID: PMC6723241 DOI: 10.3390/microorganisms7080232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/15/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
Alkaline phosphatase (AP) enables marine phytoplankton to utilize dissolved organic phosphorus (DOP) when dissolved inorganic phosphate (DIP) is depleted in the ocean. Dinoflagellate AP (Dino-AP) represents a newly classified atypical type of AP, PhoAaty. Despite While being a conventional AP, PhoAEC is known to recruit Zn2+ and Mg2+ in the active center, and the cofactors required by PhoAaty have been contended and remain unclear. In this study, we investigated the metal ion requirement of AP in five dinoflagellate species. After AP activity was eliminated by using EDTA to chelate metal ions, the enzymatic activity could be recovered by the supplementation of Ca2+, Mg2+ and Mn2+ in all cases but not by that of Zn2+. Furthermore, the same analysis conducted on the purified recombinant ACAAP (AP of Amphidinium carterae) verified that the enzyme could be activated by Ca2+, Mg2+, and Mn2+ but not Zn2+. We further developed an antiserum against ACAAP, and a western blot analysis using this antibody showed a remarkable up-regulation of ACAAP under a phosphate limitation, consistent with elevated AP activity. The unconventional metal cofactor requirement of Dino-AP may be an adaptation to trace metal limitations in the ocean, which warrants further research to understand the niche differentiation between dinoflagellates and other phytoplankton that use Zn–Mg AP in utilizing DOP.
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71
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Cáceres C, Spatharis S, Kaiserli E, Smeti E, Flowers H, Bonachela JA. Temporal phosphate gradients reveal diverse acclimation responses in phytoplankton phosphate uptake. ISME JOURNAL 2019; 13:2834-2845. [PMID: 31350454 DOI: 10.1038/s41396-019-0473-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 06/11/2019] [Accepted: 06/28/2019] [Indexed: 11/10/2022]
Abstract
Phytoplankton face environmental nutrient variations that occur in the dynamic upper layers of the ocean. Phytoplankton cells are able to rapidly acclimate to nutrient fluctuations by adjusting their nutrient-uptake system and metabolism. Disentangling these acclimation responses is a critical step in bridging the gap between phytoplankton cellular physiology and community ecology. Here, we analyzed the dynamics of phosphate (P) uptake acclimation responses along different P temporal gradients by using batch cultures of the diatom Phaeodactylum tricornutum. We employed a multidisciplinary approach that combined nutrient-uptake bioassays, transcriptomic analysis, and mathematical models. Our results indicated that cells increase their maximum nutrient-uptake rate (Vmax) both in response to P pulses and strong phosphorus limitation. The upregulation of three genes coding for different P transporters in cells experiencing low intracellular phosphorus levels supported some of the observed Vmax variations. In addition, our mathematical model reproduced the empirical Vmax patterns by including two types of P transporters upregulated at medium-high environmental and low intracellular phosphorus levels, respectively. Our results highlight the existence of a sequence of acclimation stages along the phosphate continuum that can be understood as a succession of acclimation responses. We provide a novel conceptual framework that can contribute to integrating and understanding the dynamics and wide diversity of acclimation responses developed by phytoplankton.
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Affiliation(s)
- Carlos Cáceres
- Department of Mathematics and Statistics, University of Strathclyde, Livingstone Tower, 26 Richmond St., Glasgow, Scotland, G1 1XH, UK. .,Schiermeier Olentangy River Wetland Research Park, School of Environment and Natural Resources, The Ohio State University, Columbus, OH, 43202, USA.
| | - Sofie Spatharis
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, G12 8QQ, UK.,School of Life Sciences, University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Evangelia Smeti
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, 46.7 km Athens-Sounio Ave., Anavyssos, 19013, Greece
| | - Hugh Flowers
- Department of Chemistry, University of Glasgow, Glasgow, Scotland, G12 8QQ, UK
| | - Juan A Bonachela
- Department of Mathematics and Statistics, University of Strathclyde, Livingstone Tower, 26 Richmond St., Glasgow, Scotland, G1 1XH, UK. .,Department of Ecology, Evolution, and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ, 08901, USA.
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Kokabi K, Gorelova O, Ismagulova T, Itkin M, Malitsky S, Boussiba S, Solovchenko A, Khozin-Goldberg I. Metabolomic foundation for differential responses of lipid metabolism to nitrogen and phosphorus deprivation in an arachidonic acid-producing green microalga. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:95-115. [PMID: 31128719 DOI: 10.1016/j.plantsci.2019.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/05/2019] [Accepted: 02/11/2019] [Indexed: 05/08/2023]
Abstract
The green oleaginous microalga Lobosphaera incisa accumulates storage lipids triacylglycerols (TAG) enriched in the long-chain polyunsaturated fatty acid arachidonic acid under nitrogen (N) deprivation. In contrast, under phosphorous (P) deprivation, the production of the monounsaturated oleic acid prevails. We compared physiological responses, ultrastructural, and metabolic consequences of L. incisa acclimation to N and P deficiency to provide novel insights into the key determinants of ARA accumulation. Differential responses to nutrient deprivation on growth performance, carbon-to-nitrogen stoichiometry, membrane lipid composition and TAG accumulation were demonstrated. Ultrastructural analyses suggested a dynamic role for vacuoles in sustaining cell homeostasis under conditions of different nutrient availability and their involvement in autophagy in L. incisa. Paralleling ARA-rich TAG accumulation in lipid droplets, N deprivation triggered intensive chloroplast dismantling and promoted catabolic processes. Metabolome analysis revealed depletion of amino acids and pyrimidines, and repression of numerous biosynthetic hubs to favour TAG biosynthesis under N deprivation. Under P deprivation, despite the relatively low growth penalties, the presence of the endogenous P reserves and the characteristic lipid remodelling, metabolic signatures of energy deficiency were revealed. Metabolome adjustments to P deprivation included depletion in ATP and phosphorylated nucleotides, increased levels of TCA-cycle intermediates and osmoprotectants. We conclude that characteristic cellular and metabolome adjustments tailor the adaptive responses of L. incisa to N and P deprivation modulating its LC-PUFA production.
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Affiliation(s)
- Kamilya Kokabi
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Olga Gorelova
- Department of Bioengineering, Faculty of Biology, Moscow State University, GSP-1, Moscow, 119234, Russia
| | - Tatiana Ismagulova
- Department of Bioengineering, Faculty of Biology, Moscow State University, GSP-1, Moscow, 119234, Russia
| | - Maxim Itkin
- Metabolic Profiling Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Metabolic Profiling Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Alexei Solovchenko
- Department of Bioengineering, Faculty of Biology, Moscow State University, GSP-1, Moscow, 119234, Russia; Peoples Friendship University of Russia (RUDN University), Moscow, 117198, Russia
| | - Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel.
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73
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Thangaraj S, Shang X, Sun J, Liu H. Quantitative Proteomic Analysis Reveals Novel Insights into Intracellular Silicate Stress-Responsive Mechanisms in the Diatom Skeletonema dohrnii. Int J Mol Sci 2019; 20:E2540. [PMID: 31126124 PMCID: PMC6566588 DOI: 10.3390/ijms20102540] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/19/2019] [Accepted: 05/20/2019] [Indexed: 01/04/2023] Open
Abstract
Diatoms are a successful group of marine phytoplankton that often thrives under adverse environmental stress conditions. Members of the Skeletonema genus are ecologically important which may subsist during silicate stress and form a dense bloom following higher silicate concentration. However, our understanding of diatoms' underlying molecular mechanism involved in these intracellular silicate stress-responses are limited. Here an iTRAQ-based proteomic method was coupled with multiple physiological techniques to explore distinct cellular responses associated with oxidative stress in the diatom Skeletonema dohrnii to the silicate limitation. In total, 1768 proteins were detected; 594 proteins were identified as differentially expressed (greater than a two-fold change; p < 0.05). In Si-limited cells, downregulated proteins were mainly related to photosynthesis metabolism, light-harvesting complex, and oxidative phosphorylation, corresponding to inducing oxidative stress, and ROS accumulation. None of these responses were identified in Si-limited cells; in comparing with other literature, Si-stress cells showed that ATP-limited diatoms are unable to rely on photosynthesis, which will break down and reshuffle carbon metabolism to compensate for photosynthetic carbon fixation losses. Our findings have a good correlation with earlier reports and provides a new molecular level insight into the systematic intracellular responses employed by diatoms in response to silicate stress in the marine environment.
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Affiliation(s)
- Satheeswaran Thangaraj
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Faculty of Food Engineering and Biotechnology, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
| | - Xiaomei Shang
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
| | - Jun Sun
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
| | - Haijiao Liu
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, No 29, 13th Avenue, TEDA, Tianjin 300457, China.
- Institute of Marine Science and Technology, Shandong University, No 27, Shanda Nan Road, Jinan 250110, China.
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74
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Diaz JM, Steffen R, Sanders JG, Tang Y, Duhamel S. Preferential utilization of inorganic polyphosphate over other bioavailable phosphorus sources by the model diatoms Thalassiosira spp. Environ Microbiol 2019; 21:2415-2425. [PMID: 30972877 PMCID: PMC6849833 DOI: 10.1111/1462-2920.14630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 11/28/2022]
Abstract
Polyphosphates and phosphomonoesters are dominant components of marine dissolved organic phosphorus (DOP). Collectively, DOP represents an important nutritional phosphorus (P) source for phytoplankton growth in the ocean, but the contribution of specific DOP sources to microbial community P demand is not fully understood. In a prior study, it was reported that inorganic polyphosphate was not bioavailable to the model diatoms Thalassiosira weissflogii and Thalassiosira pseudonana. However, in this study, we show that the previous finding was a misinterpretation based on a technical artefact of media preparation and that inorganic polyphosphate is actually widely bioavailable to Thalassiosira spp. In fact, orthophosphate, inorganic tripolyphosphate (3polyP), adenosine triphosphate (ATP) and adenosine monophosphate supported equivalent growth rates and final growth yields within each of four strains of Thalassiosira spp. However, enzyme activity assays revealed in all cultures that cell-associated hydrolysis rates of 3polyP were typically more than ~10-fold higher than degradation of ATP and the model phosphomonoester compound 4-methylumbelliferyl phosphate. These results build on prior work, which showed the preferential utilization of polyphosphates in the cell-free exudates of Thalassiosira spp., and suggest that inorganic polyphosphates may be a key bioavailable source of P for marine phytoplankton.
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Affiliation(s)
- Julia M Diaz
- Skidaway Institute of Oceanography, Department of Marine Sciences, University of Georgia, Savannah, GA, USA
| | - Rachel Steffen
- Skidaway Institute of Oceanography, Department of Marine Sciences, University of Georgia, Savannah, GA, USA
| | - James G Sanders
- Skidaway Institute of Oceanography, Department of Marine Sciences, University of Georgia, Savannah, GA, USA
| | - Yuanzhi Tang
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Solange Duhamel
- Lamont-Doherty Earth Observatory, Division of Biology and Paleo Environment, Palisades, NY, USA
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75
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Cheregi O, Ekendahl S, Engelbrektsson J, Strömberg N, Godhe A, Spetea C. Microalgae biotechnology in Nordic countries - the potential of local strains. PHYSIOLOGIA PLANTARUM 2019; 166:438-450. [PMID: 30809828 PMCID: PMC6850598 DOI: 10.1111/ppl.12951] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 05/03/2023]
Abstract
Climate change, energy use and food security are the main challenges that our society is facing nowadays. Biofuels and feedstock from microalgae can be part of the solution if high and continuous production is to be ensured. This could be attained in year-round, low cost, outdoor cultivation systems using strains that are not only champion producers of desired compounds but also have robust growth in a dynamic climate. Using microalgae strains adapted to the local conditions may be advantageous particularly in Nordic countries. Here, we review the current status of laboratory and outdoor-scale cultivation in Nordic conditions of local strains for biofuel, high-value compounds and water remediation. Strains suitable for biotechnological purposes were identified from the large and diverse pool represented by saline (NE Atlantic Ocean), brackish (Baltic Sea) and fresh water (lakes and rivers) sources. Energy-efficient annual rotation for cultivation of strains well adapted to Nordic climate has the potential to provide high biomass yields for biotechnological purposes.
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Affiliation(s)
- Otilia Cheregi
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburg 40530Sweden
| | - Susanne Ekendahl
- Department of Chemistry and MaterialsRISE Research Institutes of SwedenBorås 50115Sweden
| | - Johan Engelbrektsson
- Department of Chemistry and MaterialsRISE Research Institutes of SwedenBorås 50115Sweden
| | - Niklas Strömberg
- Department of Chemistry and MaterialsRISE Research Institutes of SwedenBorås 50115Sweden
| | - Anna Godhe
- Department of Marine SciencesUniversity of GothenburgGothenburg 40530Sweden
| | - Cornelia Spetea
- Department of Biological and Environmental SciencesUniversity of GothenburgGothenburg 40530Sweden
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76
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Wan L, Chen X, Deng Q, Yang L, Li X, Zhang J, Song C, Zhou Y, Cao X. Phosphorus strategy in bloom-forming cyanobacteria (Dolichospermum and Microcystis) and its role in their succession. HARMFUL ALGAE 2019; 84:46-55. [PMID: 31128812 DOI: 10.1016/j.hal.2019.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
Dolichospermum (formerly Anabaena) and Microcystis cause harmful cyanobacterial blooms in freshwater ecosystems worldwide. Input reduction of both nitrogen (N) and phosphorus (P) are commonly recognized as basic ways of controlling blooms, but little is known about the roles of nutrients and their using strategy among cyanobacteria in triggering the succession of diazotrophic to non-diazotrophic cyanobacteria. In this study, we investigated in situ responses of cyanobactria to ambient P status during the transition from Dolichospermum flos-aquae to Microcystis spp. in Lake Taihu and Lake Chaohu. While dominant in phytoplankton community, D. flos-aquae experienced P deficiency as evidenced by qualitative detection of extracellular phosphatase via enzyme labeled fluorescence (ELF). The percentage of ELF-labelled D. flos-aquae cells was 33% when it dominated the phytoplankton community, and was 78% when it co-dominated with Microcystis spp., indicating an increase in P deficiency. Meanwhile, no ELF-labelled Microcystis cells were observed while polyphosphate body (PPB) were present, suggesting that Microcystis spp. were not P deficient. Additionally, the percentages of Microcystis cells containing PPB showed an inverted "U-shaped" relationship with concentrations on soluble reactive phosphorus (SRP). To validate the field observation, a laboratory study of the monocultures of the dominant cyanobacteria was conducted. Extracellular alkaline phosphatase activity (APA) and PPB accumulation were regulated by P availability in monocultures of D. flos-aquae. Interestingly, no cell bound extracellular phosphatase was found on Microcystis aeruginasa even in the culture without P supply. Consistently, the expressions of phosphatase encoding gene phoX showed no differences among the treatments. The way in which PPB accumulation occurred in Microcystis spp. in response to P availability in the cultures was similar to that observed in the field, demonstrating a strategy of energy conservation over P accumulation. The competitive advantage of Microcystis spp. was displayed at low P concentrations: where it could rapidly uptake and store inorganic P, which also increased the P deficiency of the coexisting phytoplankton species. Responses of P-transport gene pstS confirmed this hypothesis. The physiological and molecular mechanisms mentioned above enable Microcystis to survive and proliferate in environment with low available P supply more efficiently. In conclusion, different cyanobacterial species have distinct ways of responding to P availability, suggesting that the control of cyanobacterial blooms by targeted nutrient reduction is largely dependent upon the dominant species. P reduction is more effective in controlling diazotrophic cyanobacteria than non-diazotrophic cyanobacteria.
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Affiliation(s)
- Lingling Wan
- Key Laboratory of Algal Biology, State key laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Xiaoyan Chen
- Key Laboratory of Algal Biology, State key laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Qinghui Deng
- Key Laboratory of Algal Biology, State key laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Liu Yang
- Key Laboratory of Algal Biology, State key laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Xiaowen Li
- Key Laboratory of Algal Biology, State key laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Junyi Zhang
- Wuxi Environmental Monitoring Centre, Wuxi, 214121, PR China
| | - Chunlei Song
- Key Laboratory of Algal Biology, State key laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Yiyong Zhou
- Key Laboratory of Algal Biology, State key laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Xiuyun Cao
- Key Laboratory of Algal Biology, State key laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
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77
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Dong C, Zhang H, Yang Y, He X, Liu L, Fu J, Shi J, Wu Z. Physiological and transcriptomic analyses to determine the responses to phosphorus utilization in Nostoc sp. HARMFUL ALGAE 2019; 84:10-18. [PMID: 31128794 DOI: 10.1016/j.hal.2019.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 03/05/2019] [Accepted: 03/08/2019] [Indexed: 05/05/2023]
Abstract
Phosphorus (P) is an important factor driving algal growth in aquatic ecosystems. In the present study, the growth, P uptake and utilization, photosynthesis, and transcriptome profile of Nostoc sp. were measured when Nostoc sp. cultured in media containing β-glycerol phosphate (β-gly, containing COP bonds), 2-aminoethylphosphonic acid (2-amin, containing CP bonds), or orthophosphate (K2HPO4), and in P-free (NP) medium. The results revealed that NP treatment adversely affected the growth and photosynthesis of Nostoc sp. and significantly down-regulated the expression of genes related to nutrient transport and material metabolism. Furthermore, 2-amin treatment reduced the growth of Nostoc sp. but did not significantly reduce photosynthesis, and the treatments of NP and 2-amin up-regulated the expressions of genes related antioxidation and stress. Additionally, there were no obvious differences in growth, photosynthesis, and phosphorus utilization between the β-gly and K2HPO4 treatments. These results suggested that Nostoc had a flexible ability to utilize P, which might play an important role in its widespread distribution in the environment.
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Affiliation(s)
- Congcong Dong
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Hongbo Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Yanjun Yang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Xinyu He
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Li Liu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Junke Fu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Junqiong Shi
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Zhongxing Wu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Ecology and Resources Research in Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, PR China.
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78
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Watson SJ, Needoba JA, Peterson TD. Widespread detection of Candidatus Accumulibacter phosphatis, a polyphosphate-accumulating organism, in sediments of the Columbia River estuary. Environ Microbiol 2019; 21:1369-1382. [PMID: 30815950 DOI: 10.1111/1462-2920.14576] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/11/2019] [Accepted: 02/26/2019] [Indexed: 11/27/2022]
Abstract
Enhanced biological phosphorus removal (EBPR) exploits the metabolism of polyphosphate-accumulating organisms (PAOs) to remove excess phosphorus (P) from wastewater treatment. Candidatus Accumulibacter phosphatis (Accumulibacter) is the most abundant and well-studied PAO in EBPR systems. In a previous study, we detected polyphosphates throughout peripheral bay sediments, and hypothesized that an estuary is an ideal setting to evaluate PAOs in a natural system, given that estuaries are characterized by dynamic dissolved oxygen fluctuations that potentially favour PAO metabolism. We detected nucleotide sequences attributable to Accumulibacter (16S rRNA, ppk1) in sediments within three peripheral bays of the Columbia River estuary at abundances rivalling those observed in conventional wastewater treatment plants (0.01%-2.6%). Most of the sequences attributable to Accumulibacter were Type I rather than Type II, despite the fact that the estuary does not have particularly high nutrient concentrations. The highest diversity of Accumulibacter was observed in oligohaline peripheral bays, while the greatest abundances were observed at the mouth of the estuary in mesohaline sediments in the spring and summer. In addition, an approximately 70% increase in polyphosphate concentrations observed at one of the sites between dawn and dusk suggests that PAOs may play an important role in P cycling in estuary sediments.
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Affiliation(s)
- Sheree J Watson
- Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
| | - Joseph A Needoba
- Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA.,OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, USA
| | - Tawnya D Peterson
- Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA.,OHSU-PSU School of Public Health, Oregon Health & Science University, Portland, OR, USA
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79
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Saito MA, Bertrand EM, Duffy ME, Gaylord DA, Held NA, Hervey WJ, Hettich RL, Jagtap PD, Janech MG, Kinkade DB, Leary DH, McIlvin MR, Moore EK, Morris RM, Neely BA, Nunn BL, Saunders JK, Shepherd AI, Symmonds NI, Walsh DA. Progress and Challenges in Ocean Metaproteomics and Proposed Best Practices for Data Sharing. J Proteome Res 2019; 18:1461-1476. [PMID: 30702898 DOI: 10.1021/acs.jproteome.8b00761] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, colimitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries. Yet challenges remain for ocean metaproteomics due to the great biological diversity that produces highly complex mass spectra, as well as the difficulty in obtaining and working with environmental samples. This review summarizes the progress and challenges facing ocean metaproteomic scientists and proposes best practices for data sharing of ocean metaproteomic data sets, including the data types and metadata needed to enable intercomparisons of protein distributions and annotations that could foster global ocean metaproteomic capabilities.
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Affiliation(s)
- Mak A Saito
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Erin M Bertrand
- Department of Biology , Dalhousie University , Halifax , Nova Scotia B3H 4R2 , Canada
| | - Megan E Duffy
- School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - David A Gaylord
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Noelle A Held
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | | | - Robert L Hettich
- Oak Ridge National Laboratory and Microbiology Department , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Saint Paul , Minnesota 55108 , United States
| | - Michael G Janech
- College of Charleston , Charleston , South Carolina 29424 , United States
| | - Danie B Kinkade
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Dagmar H Leary
- U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States
| | - Matthew R McIlvin
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Eli K Moore
- Department of Environmental Science , Rowan University , Glassboro , New Jersey 08028 , United States
| | - Robert M Morris
- School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - Benjamin A Neely
- National Institute of Standards and Technology , Charleston , South Carolina 29412 , United States
| | - Brook L Nunn
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Jaclyn K Saunders
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States.,School of Oceanography , University of Washington , Seattle , Washington 98195-7940 , United States
| | - Adam I Shepherd
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - Nicholas I Symmonds
- Woods Hole Oceanographic Institution , Woods Hole , Massachusetts 02543 , United States
| | - David A Walsh
- Department of Biology , Concordia University , Montreal , Quebec H4B 1R6 , Canada
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80
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Frischkorn KR, Haley ST, Dyhrman ST. Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the N 2 Fixing Cyanobacterium Trichodesmium erythraeum. Front Microbiol 2019; 10:330. [PMID: 30891009 PMCID: PMC6411698 DOI: 10.3389/fmicb.2019.00330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/08/2019] [Indexed: 01/27/2023] Open
Abstract
The N2 fixing cyanobacterium Trichodesmium is a critically important organism in oligotrophic marine ecosystems, supplying “new” nitrogen (N) to the otherwise N-poor tropical and subtropical regions where it occurs. Low concentrations of phosphorus (P) in these regions can constrain Trichodesmium distribution and N2 fixation rates. Physiological characterization of a single species in a mixed community can be challenging, and ‘omic approaches are increasingly important tools for tracking nutritional physiology in a taxon-specific manner. As such, studies examining the dynamics of gene and protein markers of physiology (e.g., nutrient stress) are critical for the application and interpretation of such ‘omic data in situ. Here we leveraged combined transcriptomics, proteomics, and enzyme activity assays to track the physiological response of Trichodesmium erythraeum IMS101 to P deficiency and subsequent P re-supply over 72 h of sampling. P deficiency resulted in differential gene expression, protein abundance, and enzyme activity that highlighted a synchronous shift in P physiology with increases in the transcripts and corresponding proteins for hydrolyzing organic phosphorus, taking up phosphate with higher affinity, and modulating intracellular P demand. After P deficiency was alleviated, gene expression of these biomarkers was reduced to replete levels within 4 h of P amendment. A number of these gene biomarkers were adjacent to putative pho boxes and their expression patterns were similar to a sphR response regulator. Protein products of the P deficiency biomarkers were slow to decline, with 84% of the original P deficient protein set still significantly differentially expressed after 72 h. Alkaline phosphatase activity tracked with proteins for this enzyme. With the rapid turnover time of transcripts, they appear to be good biomarkers of a P stress phenotype, whereas proteins, with a slower turnover time, may better reflect cellular activities. These results highlight the importance of validating and pairing transcriptome and proteome data that can be applied to physiological studies of key species in situ.
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Affiliation(s)
- Kyle R Frischkorn
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.,Lamont-Doherty Earth Observatory, Palisades, NY, United States
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Palisades, NY, United States
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.,Lamont-Doherty Earth Observatory, Palisades, NY, United States
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81
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Chiriboga O, Rorrer GL. Phosphate addition strategies for enhancing the co-production of lipid and chitin nanofibers during fed-batch cultivation of the diatom Cyclotella sp. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.101403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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82
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Wurch LL, Alexander H, Frischkorn KR, Haley ST, Gobler CJ, Dyhrman ST. Transcriptional Shifts Highlight the Role of Nutrients in Harmful Brown Tide Dynamics. Front Microbiol 2019; 10:136. [PMID: 30809203 PMCID: PMC6379262 DOI: 10.3389/fmicb.2019.00136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/21/2019] [Indexed: 11/13/2022] Open
Abstract
Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy, as nutrient concentrations often suggest coastal blooms are nitrogen-limited. However, defining best nutrient management practices is a long-standing challenge: in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data demonstrate the importance of phosphorus in controlling brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations alone were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.
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Affiliation(s)
- Louie L Wurch
- Department of Biology, James Madison University, Harrisonburg, VA, United States
| | - Harriet Alexander
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Kyle R Frischkorn
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Sheean T Haley
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States
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83
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Non-linear Physiology and Gene Expression Responses of Harmful Alga Heterosigma akashiwo to Rising CO2. Protist 2019; 170:38-51. [DOI: 10.1016/j.protis.2018.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/02/2018] [Accepted: 10/15/2018] [Indexed: 11/22/2022]
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84
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Coordinated downregulation of the photosynthetic apparatus as a protective mechanism against UV exposure in the diatom Corethron hystrix. Appl Microbiol Biotechnol 2019; 103:1837-1850. [PMID: 30617536 DOI: 10.1007/s00253-018-9544-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/07/2018] [Accepted: 11/25/2018] [Indexed: 10/27/2022]
Abstract
The effect of ultraviolet radiation (UVR) on photosynthetic efficiency and the resulting mechanisms against UV exposure employed by phytoplankton are not completely understood. To address this knowledge gap, we developed a novel close-coupled, wavelength-configurable platform designed to produce precise and repeatable in vitro irradiation of Corethron hystrix, a member of a genera found abundantly in the Southern Ocean where UV exposure is high. We aimed to determine its metabolic, protective, and repair mechanisms as a function of varying levels of specific electromagnetic energy. Our results show that the physiological responses to each energy level of UV have a negative linear decrease in the photosynthetic efficiency of photosystem II proportional to UV intensity, corresponding to a large increase in the turnover time of quinone reoxidation. Gene expression changes of photosystem II-related reaction center proteins D1, CP43, and CP47 showed coordinated downregulation whereas the central metabolic pathway demonstrated mixed expression of up and downregulated transcripts after UVR exposure. These results suggest that while UVR may damage photosynthetic machinery, oxidative damage may limit production of new photosynthetic and electron transport complexes as a result of UVR exposure.
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85
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Schoffelen NJ, Mohr W, Ferdelman TG, Littmann S, Duerschlag J, Zubkov MV, Ploug H, Kuypers MMM. Single-cell imaging of phosphorus uptake shows that key harmful algae rely on different phosphorus sources for growth. Sci Rep 2018; 8:17182. [PMID: 30464246 PMCID: PMC6249326 DOI: 10.1038/s41598-018-35310-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 11/02/2018] [Indexed: 12/04/2022] Open
Abstract
Single-cell measurements of biochemical processes have advanced our understanding of cellular physiology in individual microbes and microbial populations. Due to methodological limitations, little is known about single-cell phosphorus (P) uptake and its importance for microbial growth within mixed field populations. Here, we developed a nanometer-scale secondary ion mass spectrometry (nanoSIMS)-based approach to quantify single-cell P uptake in combination with cellular CO2 and N2 fixation. Applying this approach during a harmful algal bloom (HAB), we found that the toxin-producer Nodularia almost exclusively used phosphate for growth at very low phosphate concentrations in the Baltic Sea. In contrast, the non-toxic Aphanizomenon acquired only 15% of its cellular P-demand from phosphate and ~85% from organic P. When phosphate concentrations were raised, Nodularia thrived indicating that this toxin-producer directly benefits from phosphate inputs. The phosphate availability in the Baltic Sea is projected to rise and therefore might foster more frequent and intense Nodularia blooms with a concomitant rise in the overall toxicity of HABs in the Baltic Sea. With a projected increase in HABs worldwide, the capability to use organic P may be a critical factor that not only determines the microbial community structure, but the overall harmfulness and associated costs of algal blooms.
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Affiliation(s)
- Niels J Schoffelen
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Wiebke Mohr
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| | - Timothy G Ferdelman
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia Duerschlag
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mikhail V Zubkov
- Ocean Biogeochemistry and Ecosystems, National Oceanography Centre Southampton, European Way, Southampton, SO14 3ZH, United Kingdom.,Scottish Association for Marine Science, Oban, Argyll PA37 1QA, Scotland, United Kingdom
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Carl Skottsbergs Gata 22B, 41319, Gothenburg, Sweden
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
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86
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Chen XH, Li YY, Zhang H, Liu JL, Xie ZX, Lin L, Wang DZ. Quantitative Proteomics Reveals Common and Specific Responses of a Marine Diatom Thalassiosira pseudonana to Different Macronutrient Deficiencies. Front Microbiol 2018; 9:2761. [PMID: 30487787 PMCID: PMC6246746 DOI: 10.3389/fmicb.2018.02761] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/29/2018] [Indexed: 11/13/2022] Open
Abstract
Macronutrients such as nitrogen (N), phosphorus (P), and silicon (Si) are essential for the productivity and distribution of diatoms in the ocean. Responses of diatoms to a particular macronutrient deficiency have been investigated, however, we know little about their common or specific responses to different macronutrients. Here, we investigated the physiology and quantitative proteomics of a diatom Thalassiosira pseudonana grown in nutrient-replete, N-, P-, and Si-deficient conditions. Cell growth was ceased in all macronutrient deficient conditions while cell volume and cellular C content under P- and Si-deficiencies increased. Contents of chlorophyll a, protein and cellular N decreased in both N- and P-deficient cells but chlorophyll a and cellular N increased in the Si-deficient cells. Cellular P content increased under N- and Si-deficiencies. Proteins involved in carbon fixation and photorespiration were down-regulated under all macronutrient deficiencies while neutral lipid synthesis and carbohydrate accumulation were enhanced. Photosynthesis, chlorophyll biosynthesis, and protein biosynthesis were down-regulated in both N- and P-deficient cells, while Si transporters, light-harvesting complex proteins, chloroplastic ATP synthase, plastid transcription and protein synthesis were up-regulated in the Si-deficient cells. Our results provided insights into the common and specific responses of T. pseudonana to different macronutrient deficiencies and identified specific proteins potentially indicating a particular macronutrient deficiency.
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Affiliation(s)
- Xiao-Huang Chen
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuan-Yuan Li
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Hao Zhang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jiu-Ling Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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87
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Bílková B, Świderská Z, Zita L, Laloë D, Charles M, Beneš V, Stopka P, Vinkler M. Domestic Fowl Breed Variation in Egg White Protein Expression: Application of Proteomics and Transcriptomics. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11854-11863. [PMID: 30296079 DOI: 10.1021/acs.jafc.8b03099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Avian egg white is essential for protecting and nourishing bird embryos during their development. Being produced in the female magnum, variability in hen oviduct gene expression may affect egg white composition in domestic chickens. Since traditional poultry breeds may represent a source of variation, in the present study we describe the egg white proteome (mass spectrometry) and corresponding magnum transcriptome (high-throughput sequencing) for 20 hens from five domestic fowl breeds (large breeds: Araucana, Czech golden pencilled, Minorca; and small breeds: Booted bantam, Rosecomb bantam). In total, we identified 189 egg white proteins and 16391 magnum-expressed genes. The majority of egg white protein content comprised proteins with an antimicrobial function. Despite general similarity, Between-class Principal Component Analysis revealed significant breed-specific variability in protein abundances, differentiating especially small and large breeds. Though we found strong association between magnum mRNA expression and egg white protein abundance across genes, coinertia analysis revealed no transcriptome/proteome costructure at the individual level. Our study is the first to show variation in protein abundances in egg white across chicken breeds with potential effects on egg quality, biosafety, and chick development. The observed interindividual variation probably results from post-transcriptional regulation creating a discrepancy between proteomic and transcriptomic data.
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Affiliation(s)
- Barbora Bílková
- Charles University , Faculty of Science, Department of Zoology , Prague , Czech Republic
| | - Zuzana Świderská
- Charles University , Faculty of Science, Department of Zoology , Prague , Czech Republic
- Charles University , Faculty of Science, Department of Cell Biology , Prague , Czech Republic
| | - Lukáš Zita
- Czech University of Life Sciences , Faculty of Agrobiology, Food and Natural Resources, Department of Animal Science , Prague , Czech Republic
| | - Denis Laloë
- GABI, INRA, AgroParisTech , Université Paris-Saclay , Jouy-en-Josas , France
| | - Mathieu Charles
- GABI, INRA, AgroParisTech , Université Paris-Saclay , Jouy-en-Josas , France
| | - Vladimír Beneš
- European Molecular Biology Laboratory , Heidelberg 69117 , Germany
| | - Pavel Stopka
- Charles University , Faculty of Science, Department of Zoology , Prague , Czech Republic
| | - Michal Vinkler
- Charles University , Faculty of Science, Department of Zoology , Prague , Czech Republic
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88
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Proteome evolution under non-substitutable resource limitation. Nat Commun 2018; 9:4650. [PMID: 30405128 PMCID: PMC6220234 DOI: 10.1038/s41467-018-07106-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 10/10/2018] [Indexed: 12/12/2022] Open
Abstract
Resource limitation is a major driver of the ecological and evolutionary dynamics of organisms. Short-term responses to resource limitation include plastic changes in molecular phenotypes including protein expression. Yet little is known about the evolution of the molecular phenotype under longer-term resource limitation. Here, we combine experimental evolution of the green alga Chlamydomonas reinhardtii under multiple different non-substitutable resource limitation regimes with proteomic measurements to investigate evolutionary adaptation of the molecular phenotype. We demonstrate convergent proteomic evolution of core metabolic functions, including the Calvin-Benson cycle and gluconeogenesis, across different resource limitation environments. We do not observe proteomic changes consistent with optimized uptake of particular limiting resources. Instead, we report that adaptation proceeds in similar directions under different types of non-substitutable resource limitation. This largely convergent evolution of the expression of core metabolic proteins is associated with an improvement in the resource assimilation efficiency of nitrogen and phosphorus into biomass. Organisms could respond to essential resource limitation by increasing metabolic efficiency or resource acquisition ability. Here, the authors experimentally evolve green algae under different resource limitations and show convergent evolution of core metabolism rather than resource specialization.
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89
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Remmers IM, D'Adamo S, Martens DE, de Vos RC, Mumm R, America AH, Cordewener JH, Bakker LV, Peters SA, Wijffels RH, Lamers PP. Orchestration of transcriptome, proteome and metabolome in the diatom Phaeodactylum tricornutum during nitrogen limitation. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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90
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Cohen NR, Gong W, Moran DM, McIlvin MR, Saito MA, Marchetti A. Transcriptomic and proteomic responses of the oceanic diatom
Pseudo‐nitzschia granii
to iron limitation. Environ Microbiol 2018; 20:3109-3126. [DOI: 10.1111/1462-2920.14386] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 08/09/2018] [Accepted: 08/12/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Natalie R Cohen
- Department of Marine Sciences University of North Carolina at Chapel Hill Chapel Hill NC 27514 USA
- Marine Chemistry and Geochemistry Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Weida Gong
- Department of Marine Sciences University of North Carolina at Chapel Hill Chapel Hill NC 27514 USA
| | - Dawn M. Moran
- Marine Chemistry and Geochemistry Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Matthew R. McIlvin
- Marine Chemistry and Geochemistry Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Mak A. Saito
- Marine Chemistry and Geochemistry Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Adrian Marchetti
- Department of Marine Sciences University of North Carolina at Chapel Hill Chapel Hill NC 27514 USA
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91
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Li T, Guo C, Zhang Y, Wang C, Lin X, Lin S. Identification and Expression Analysis of an Atypical Alkaline Phosphatase in Emiliania huxleyi. Front Microbiol 2018; 9:2156. [PMID: 30283412 PMCID: PMC6156274 DOI: 10.3389/fmicb.2018.02156] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 08/23/2018] [Indexed: 12/21/2022] Open
Abstract
Emiliania huxleyi, a cosmopolitan coccolithophore in the modern ocean, plays an important role in the carbon cycle and local climate feedback as it can form extensive blooms, calcify, and produce dimethylsulfoniopropionate (DMSP) leading to the generation of dimethyl sulfide (DMS) which affects climate when oxidized in the atmosphere. It is known to be able to utilize dissolved organic phosphorus (DOP) by expressing a specific type of alkaline phosphatase (EHAP1) under phosphorus-limited conditions. In this study, we identified a new alkaline phosphatase (EH-PhoAaty) in this species, which we found belongs to the newly classified PhoAaty family. The expression of this atypical phosphatase was up-regulated under P-depleted conditions at both the transcriptional and translational levels, suggesting that E. huxleyi is able to express this AP to cope with phosphorus limitation. Comparative analysis revealed different transcriptional expression dynamics between eh-PhoAaty and ehap1, although both genes exhibited inducible expression under phosphate deficiency. In addition, after AP activity was eliminated by using EDTA to chelate metal ions, we found that AP activity was recovered with the supplement of Ca2+ and Zn2+, indicative of the adoption of Ca2+ as the cofactor under Zn-P co-limited conditions, likely a result of adaptation to oceanic environments where Zn2+ is often limiting.
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Affiliation(s)
- Tangcheng Li
- State Key Laboratory of Marine Environmental Science and Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen, China
| | - Chentao Guo
- State Key Laboratory of Marine Environmental Science and Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen, China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science and Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science and Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration, Xiamen University, Xiamen, China.,Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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92
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Bachy C, Charlesworth CJ, Chan AM, Finke JF, Wong CH, Wei CL, Sudek S, Coleman ML, Suttle CA, Worden AZ. Transcriptional responses of the marine green alga Micromonas pusilla and an infecting prasinovirus under different phosphate conditions. Environ Microbiol 2018; 20:2898-2912. [PMID: 29749714 DOI: 10.1111/1462-2920.14273] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/06/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022]
Abstract
Prasinophytes are widespread marine algae for which responses to nutrient limitation and viral infection are not well understood. We studied the picoprasinophyte, Micromonas pusilla, grown under phosphate-replete (0.65 ± 0.07 d-1 ) and 10-fold lower (low)-phosphate (0.11 ± 0.04 d-1 ) conditions, and infected by the phycodnavirus MpV-SP1. Expression of 17% of Micromonas genes in uninfected cells differed by >1.5-fold (q < 0.01) between nutrient conditions, with genes for P-metabolism and the uniquely-enriched Sel1-like repeat (SLR) family having higher relative transcript abundances, while phospholipid-synthesis genes were lower in low-P than P-replete. Approximately 70% (P-replete) and 30% (low-P) of cells were lysed 24 h post-infection, and expression of ≤5.8% of host genes changed relative to uninfected treatments. Host genes for CAZymes and glycolysis were activated by infection, supporting importance in viral production, which was significantly lower in slower growing (low-P) hosts. All MpV-SP1 genes were expressed, and our analyses suggest responses to differing host-phosphate backgrounds involve few viral genes, while the temporal program of infection involves many more, and is largely independent of host-phosphate background. Our study (i) identifies genes previously unassociated with nutrient acclimation or viral infection, (ii) provides insights into the temporal program of prasinovirus gene expression by hosts and (iii) establishes cell biological aspects of an ecologically important host-prasinovirus system that differ from other marine algal-virus systems.
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Affiliation(s)
- Charles Bachy
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Christina J Charlesworth
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Amy M Chan
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jan F Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Chee-Hong Wong
- Lawrence Berkeley National Laboratory, Sequencing Technology Group, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Chia-Lin Wei
- Lawrence Berkeley National Laboratory, Sequencing Technology Group, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - Maureen L Coleman
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Curtis A Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada.,Departments of Botany, and Microbiology & Immunology, and Institute of Oceans & Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada
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93
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Hu SK, Liu Z, Alexander H, Campbell V, Connell PE, Dyhrman ST, Heidelberg KB, Caron DA. Shifting metabolic priorities among key protistan taxa within and below the euphotic zone. Environ Microbiol 2018; 20:2865-2879. [PMID: 29708635 DOI: 10.1111/1462-2920.14259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/12/2022]
Abstract
A metatranscriptome study targeting the protistan community was conducted off the coast of Southern California, at the San Pedro Ocean Time-series station at the surface, 150 m (oxycline), and 890 m to link putative metabolic patterns to distinct protistan lineages. Comparison of relative transcript abundances revealed depth-related shifts in the nutritional modes of key taxonomic groups. Eukaryotic gene expression in the sunlit surface environment was dominated by phototrophs, such as diatoms and chlorophytes, and high abundances of transcripts associated with synthesis pathways (e.g., photosynthesis, carbon fixation, fatty acid synthesis). Sub-euphotic depths (150 and 890 m) exhibited strong contributions from dinoflagellates and ciliates, and were characterized by transcripts relating to digestion or intracellular nutrient recycling (e.g., breakdown of fatty acids and V-type ATPases). These transcriptional patterns underlie the distinct nutritional modes of ecologically important protistan lineages that drive marine food webs, and provide a framework to investigate trophic dynamics across diverse protistan communities.
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Affiliation(s)
- Sarah K Hu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Zhenfeng Liu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Harriet Alexander
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, USA
| | - Victoria Campbell
- Division Allergy and Infectious Diseases, UW Medicine, Seattle, WA, USA
| | - Paige E Connell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Sciences, Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA
| | - Karla B Heidelberg
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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94
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V Bondoc KG, Lembke C, Vyverman W, Pohnert G. Selective chemoattraction of the benthic diatom Seminavis robusta to phosphate but not to inorganic nitrogen sources contributes to biofilm structuring. Microbiologyopen 2018; 8:e00694. [PMID: 30033670 PMCID: PMC6460271 DOI: 10.1002/mbo3.694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/12/2018] [Accepted: 06/20/2018] [Indexed: 11/07/2022] Open
Abstract
Diatoms frequently dominate marine and freshwater biofilms as major primary producers. Nutrient resources in these biofilms are patchily distributed and fluctuate dynamically over time. We recently reported that this spatially and temporally structured environment can be exploited by motile diatoms that use chemoattraction to dissolved silicate (dSi) under Si starvation. Here, we show that the behavioral response of diatoms is more complex and selective as cells are also responding to gradients of dissolved phosphate (dP) when starved in this nutrient. In contrast, neither nitrate nor ammonium (dN) triggers an attractive response under nitrogen limitation. Video monitoring and movement pattern analysis of the model diatom Seminavis robusta revealed that dP attraction is mediated by a combined chemokinetic and chemotactic response. After locating nutrient hotspots, the microalgae slow down and recover from the limitation. The fastest recovery in terms of growth was observed after dSi limitation. In agreement with the lack of directional response, recovery from dN limitation was slowest, indicating that no short-term benefit would be drawn by the algae from the location of transient hotspots of this resource. Our results highlight the ability of diatoms to adapt to nutrient limitation by active foraging and might explain their success in patchy benthic environments.
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Affiliation(s)
- Karen Grace V Bondoc
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany.,Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Christine Lembke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, University Gent, Gent, Belgium
| | - Georg Pohnert
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany.,Max Planck Institute for Chemical Ecology, Jena, Germany
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95
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Gonçalves S, Kahlert M, Almeida SFP, Figueira E. A freshwater diatom challenged by Zn: Biochemical, physiological and metabolomic responses of Tabellaria flocculosa(Roth) Kützing. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:959-971. [PMID: 29715753 DOI: 10.1016/j.envpol.2018.01.111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/19/2018] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
Freshwater ecosystems are under threatening anthropogenic pressures worldwide, namely by metals. Diatoms are used as water quality indicators, but the influence of micronutrients such as Zn and its impacts are poorly understood. Thus, our study aimed to elucidate the tolerance level, the cellular targets and the responses to counteract Zn toxicity of freshwater diatoms by exposing Tabellaria flocculosa, isolated from a Zn contaminated stream. Biochemical, physiological and metabolomic approaches were used. It was demonstrated that Zn is toxic to T. flocculosa at concentrations occurring in contaminated environments. At low stress (30 μg Zn/L) few alterations in the metabolome were observed, but the enzymatic (SOD, CAT) and molecular (GSH, GSSG) antioxidant systems were induced, protecting cells from oxidative stress. At moderate stress (500 μg Zn/L) the main changes occurred in the metabolome (increases in fatty acids, amino acids, terpenoids, glycerol and phosphate, decreases in sucrose and lumichrome) with a moderate increase in cell damage (LPO and PC). The concerted action of all these mechanisms resulted in a non-significant decrease of growth, explaining the survival of this T. flocculosa strain in an environment with this Zn concentration. At the highest stress level (1000 μg Zn/L) the metabolome was identical to 500 μg Zn/L, and the induction of antioxidant systems and extracellular ion chelation (exopolysaccharides, frustulins) were the main responses to the increase of Zn toxicity. However, these mechanisms were unable to effectively abrogate cellular damage and growth reduction was observed. Moreover, the decrease in sucrose and especially in lumichrome should be tested as new specific markers of Zn toxicity. The information obtained in this study can assist in environmental risk assessment policies, support the prediction of diatom behaviour in highly impacted Zn environments, such as mining scenarios, and may help develop new indices, which include alterations induced by metals.
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Affiliation(s)
- Sara Gonçalves
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Kahlert
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Salomé F P Almeida
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; GeoBioTec - GeoBioSciences, GeoTechnologies and GeoEngineering Research Centre, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Etelvina Figueira
- Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
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96
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Guo J, Wilken S, Jimenez V, Choi CJ, Ansong C, Dannebaum R, Sudek L, Milner DS, Bachy C, Reistetter EN, Elrod VA, Klimov D, Purvine SO, Wei CL, Kunde-Ramamoorthy G, Richards TA, Goodenough U, Smith RD, Callister SJ, Worden AZ. Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation. Nat Microbiol 2018; 3:781-790. [PMID: 29946165 DOI: 10.1038/s41564-018-0178-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/16/2018] [Indexed: 01/05/2023]
Abstract
Marine algae perform approximately half of global carbon fixation, but their growth is often limited by the availability of phosphate or other nutrients1,2. As oceans warm, the area of phosphate-limited surface waters is predicted to increase, resulting in ocean desertification3,4. Understanding the responses of key eukaryotic phytoplankton to nutrient limitation is therefore critical5,6. We used advanced photo-bioreactors to investigate how the widespread marine green alga Micromonas commoda grows under transitions from replete nutrients to chronic phosphate limitation and subsequent relief, analysing photosystem changes and broad cellular responses using proteomics, transcriptomics and biophysical measurements. We find that physiological and protein expression responses previously attributed to stress are critical to supporting stable exponential growth when phosphate is limiting. Unexpectedly, the abundance of most proteins involved in light harvesting does not change, but an ancient light-harvesting-related protein, LHCSR, is induced and dissipates damaging excess absorbed light as heat throughout phosphate limitation. Concurrently, a suite of uncharacterized proteins with narrow phylogenetic distributions increase multifold. Notably, of the proteins that exhibit significant changes, 70% are not differentially expressed at the mRNA transcript level, highlighting the importance of post-transcriptional processes in microbial eukaryotes. Nevertheless, transcript-protein pairs with concordant changes were identified that will enable more robust interpretation of eukaryotic phytoplankton responses in the field from metatranscriptomic studies. Our results show that P-limited Micromonas responds quickly to a fresh pulse of phosphate by rapidly increasing replication, and that the protein network associated with this ability is composed of both conserved and phylogenetically recent proteome systems that promote dynamic phosphate homeostasis. That an ancient mechanism for mitigating light stress is central to sustaining growth during extended phosphate limitation highlights the possibility of interactive effects arising from combined stressors under ocean change, which could reduce the efficacy of algal strategies for optimizing marine photosynthesis.
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Affiliation(s)
- Jian Guo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Susanne Wilken
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Department of Freshwater and Marine Ecology, University of Amsterdam, Amsterdam, the Netherlands
| | - Valeria Jimenez
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Chang Jae Choi
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Charles Ansong
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard Dannebaum
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA
| | - Lisa Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | - Charles Bachy
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | | | - Denis Klimov
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | | | - Chia-Lin Wei
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA.,The Jackson Laboratory, Farmington, CT, USA
| | - Govindarajan Kunde-Ramamoorthy
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, USA.,The Jackson Laboratory, Farmington, CT, USA
| | | | | | | | | | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA. .,Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA.
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97
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Gonçalves S, Kahlert M, Almeida SFP, Figueira E. Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 625:1234-1246. [PMID: 29996420 DOI: 10.1016/j.scitotenv.2017.12.320] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 06/08/2023]
Abstract
Metals are a recognised threat to aquatic organisms but the impact of metals such as copper (Cu) on benthic freshwater diatoms is poorly understood, even if diatoms are commonly used as water quality indicators. Our study aimed to elucidate the cellular targets of Cu toxicity and the mechanisms cells resort to counteract toxicity and to increase tolerance to Cu. A concerted approach analysing the biochemical, physiological and metabolome alterations in diatom cells was conducted by exposing the freshwater diatom Tabellaria flocculosa to 0, 0.3, 6 and 10μgCu/L. Cu was already toxic to T. flocculosa at concentrations common in environments and which are not usually considered to be contaminated (0.3μgCu/L). Under Cu impact, the metabolome of T. flocculosa changed significantly, especially at high concentrations (6 and 10μgCu/L). Cu toxicity was counteracted by increasing extracellular immobilization (EPS, frustulins), antioxidant (SOD, CAT) and detoxifying (GSTs) enzymes activity and low molecular weight antioxidants (GSH). These mechanisms were fuelled by higher energy production (increased ETS activity). At the highest Cu concentration (10μg/L), these processes were specially enhanced in an attempt to restrain the oxidative stress generated by high intracellular Cu concentrations. However, these mechanisms were not able to fully protect cells, and damage in membranes and proteins increased. Moreover, the decrease of hydroxylamine and unsaturated fatty acids and the increase of saturated fatty acids, 2-palmitoylglycerol, glycerol and diterpenoid compounds should be tested as new specific markers of Cu toxicity in future studies. This information can support the prediction of diatom behaviour in different Cu contamination levels, including highly impacted environments, such as mining scenarios, and may assist in environmental risk assessment policies and restoration programs.
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Affiliation(s)
- Sara Gonçalves
- Department of Biology, University of Aveiro, Aveiro, Portugal; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Kahlert
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Salomé F P Almeida
- Department of Biology and GeoBioTec - GeoBioSciences, GeoTechnologies and GeoEngineering Research Centre, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Etelvina Figueira
- Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal.
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98
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Downs DM, Bazurto JV, Gupta A, Fonseca LL, Voit EO. The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling. AIMS Microbiol 2018; 4:289-303. [PMID: 31294216 PMCID: PMC6604926 DOI: 10.3934/microbiol.2018.2.289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/02/2018] [Indexed: 12/23/2022] Open
Abstract
Traditional biochemical research has resulted in a good understanding of many aspects of metabolism. However, this reductionist approach is time consuming and requires substantial resources, thus raising the question whether modern metabolomics and genomics should take over and replace the targeted experiments of old. We proffer that such a replacement is neither feasible not desirable and propose instead the tight integration of modern, system-wide omics with traditional experimental bench science and dedicated computational approaches. This integration is an important prerequisite toward the optimal acquisition of knowledge regarding metabolism and physiology in health and disease. The commentary describes advantages and drawbacks of current approaches to assessing metabolism and highlights the challenges to be overcome as we strive to achieve a deeper level of metabolic understanding in the future.
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Affiliation(s)
- Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Jannell V Bazurto
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Anuj Gupta
- Department of Biomedical Engineering, Georgia Institute of Technology, 950 Atlantic Drive, Suite 2115, Atlanta, GA, 30332-2000, USA
| | - Luis L Fonseca
- Department of Biomedical Engineering, Georgia Institute of Technology, 950 Atlantic Drive, Suite 2115, Atlanta, GA, 30332-2000, USA
| | - Eberhard O Voit
- Department of Biomedical Engineering, Georgia Institute of Technology, 950 Atlantic Drive, Suite 2115, Atlanta, GA, 30332-2000, USA
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99
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Brembu T, Mühlroth A, Alipanah L, Bones AM. The effects of phosphorus limitation on carbon metabolism in diatoms. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0406. [PMID: 28717016 PMCID: PMC5516115 DOI: 10.1098/rstb.2016.0406] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2017] [Indexed: 01/26/2023] Open
Abstract
Phosphorus is an essential element for life, serving as an integral component of nucleic acids, lipids and a diverse range of other metabolites. Concentrations of bioavailable phosphorus are low in many aquatic environments. Microalgae, including diatoms, apply physiological and molecular strategies such as phosphorus scavenging or recycling as well as adjusting cell growth in order to adapt to limiting phosphorus concentrations. Such strategies also involve adjustments of the carbon metabolism. Here, we review the effect of phosphorus limitation on carbon metabolism in diatoms. Two transcriptome studies are analysed in detail, supplemented by other transcriptome, proteome and metabolite data, to gain an overview of different pathways and their responses. Phosphorus, nitrogen and silicon limitation responses are compared, and similarities and differences discussed. We use the current knowledge to propose a suggestive model for the carbon flow in phosphorus-replete and phosphorus-limited diatom cells. This article is part of the themed issue ‘The peculiar carbon metabolism in diatoms’.
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Affiliation(s)
- Tore Brembu
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Alice Mühlroth
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Leila Alipanah
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Atle M Bones
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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100
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Lipidomics of Thalassiosira pseudonana under Phosphorus Stress Reveal Underlying Phospholipid Substitution Dynamics and Novel Diglycosylceramide Substitutes. Appl Environ Microbiol 2018; 84:AEM.02034-17. [PMID: 29305510 PMCID: PMC5835749 DOI: 10.1128/aem.02034-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/21/2017] [Indexed: 02/01/2023] Open
Abstract
Phytoplankton replace phosphorus-containing lipids (P-lipids) with non-P analogues, boosting growth in P-limited oceans. In the model diatom Thalassiosira pseudonana, the substitution dynamics of lipid headgroups are well described, but those of the individual lipids, differing in fatty acid composition, are unknown. Moreover, the behavior of lipids outside the common headgroup classes and the relationship between lipid substitution and cellular particulate organic P (POP) have yet to be reported. We investigated these through the mass spectrometric lipidomics of P-replete (P+) and P-depleted (P-) T. pseudonana cultures. Nonlipidic POP was depleted rapidly by the initiation of P stress, followed by the cessation of P-lipid biosynthesis and per-cell reductions in the P-lipid levels of successive generations. Minor P-lipid degradative breakdown was observed, releasing P for other processes, but most P-lipids remained intact. This may confer an advantage on efficient heterotrophic lipid consumers in P-limited oceans. Glycerophosphatidylcholine (PC), the predominant P-lipid, was similar in composition to its betaine substitute lipid. During substitution, PC was less abundant per cell and was more highly unsaturated in composition. This may reflect underlying biosynthetic processes or the regulation of membrane biophysical properties subject to lipid substitution. Finally, levels of several diglycosylceramide lipids increased as much as 10-fold under P stress. These represent novel substitute lipids and potential biomarkers for the study of P limitation in situ, contributing to growing evidence highlighting the importance of sphingolipids in phycology. These findings contribute much to our understanding of P-lipid substitution, a powerful and widespread adaptation to P limitation in the oligotrophic ocean.IMPORTANCE Unicellular organisms replace phosphorus (P)-containing membrane lipids with non-P substitutes when P is scarce, allowing greater growth of populations. Previous research with the model diatom species Thalassiosira pseudonana grouped lipids by polar headgroups in their chemical structures. The significance of the research reported here is threefold. (i) We described the individual lipids within the headgroups during P-lipid substitution, revealing the relationships between lipid headgroups and hinting at the underlying biochemical processes. (ii) We measured total cellular P, placing P-lipid substitution in the context of the broader response to P stress and yielding insight into the implications of substitution in the marine environment. (iii) We identified lipids previously unknown in this system, revealing a new type of non-P substitute lipid, which is potentially useful as a biomarker for the investigation of P limitation in the ocean.
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