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Kamakura S, Bilcke G, Sato S. Transcriptional responses to salinity-induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis. J Phycol 2024; 60:308-326. [PMID: 38446079 DOI: 10.1111/jpy.13437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up-regulation of mechanosensitive ion channels and down-regulation of Ca2+-ATPases in cells with flat valves suggested that cytosolic Ca2+ levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up-regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up-regulation of genes encoding frustule-related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity-induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca2+ levels, and downstream responses, such as Ca2+-dependent regulation of actin dynamics and frustule-related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures.
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Affiliation(s)
- Shiho Kamakura
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Gust Bilcke
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinya Sato
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
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2
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Carrión O, Zhu XY, Williams BT, Wang J, Zhang XH, Todd JD. Molecular discoveries in microbial DMSP synthesis. Adv Microb Physiol 2023; 83:59-116. [PMID: 37507162 DOI: 10.1016/bs.ampbs.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is one of the Earth's most abundant organosulfur compounds because many marine algae, bacteria, corals and some plants produce it to high mM intracellular concentrations. In these organisms, DMSP acts an anti-stress molecule with purported roles to protect against salinity, temperature, oxidative stress and hydrostatic pressure, amongst many other reported functions. However, DMSP is best known for being a major precursor of the climate-active gases and signalling molecules dimethylsulfide (DMS), methanethiol (MeSH) and, potentially, methane, through microbial DMSP catabolism. DMSP catabolism has been extensively studied and the microbes, pathways and enzymes involved have largely been elucidated through the application of molecular research over the last 17 years. In contrast, the molecular biology of DMSP synthesis is a much newer field, with the first DMSP synthesis enzymes only being identified in the last 5 years. In this review, we discuss how the elucidation of key DMSP synthesis enzymes has greatly expanded our knowledge of the diversity of DMSP-producing organisms, the pathways used, and what environmental factors regulate production, as well as to inform on the physiological roles of DMSP. Importantly, the identification of key DMSP synthesis enzymes in the major groups of DMSP producers has allowed scientists to study the distribution and predict the importance of different DMSP-producing organisms to global DMSP production in diverse marine and sediment environments. Finally, we highlight key challenges for future molecular research into DMSP synthesis that need addressing to better understand the cycling of this important marine organosulfur compound, and its magnitude in the environment.
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Affiliation(s)
- Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
| | - Xiao-Yu Zhu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jinyan Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
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3
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de Freitas Santos da Silva AC, de Santana CO, Dos Santos Vergilio C, de Jesus TB. Distribution, toxicity and bioaccumulation of trace metals in environmental matrices of an estuary in a protected area. Mar Pollut Bull 2023; 191:114928. [PMID: 37146550 DOI: 10.1016/j.marpolbul.2023.114928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/22/2023] [Accepted: 04/07/2023] [Indexed: 05/07/2023]
Abstract
Mangroves are productive ecosystems that are highly threatened by anthropogenic activities. We investigated the environmental quality of the Serinhaém river estuary located in a legally protected area. Through chemical analysis of sediments and tissues of Cardisoma guanhumi, in addition to bioassays with elutriate involving Nitokra sp. and Thalassiosira pseudonana, we determined the contamination status and risk factors related to trace metals in the estuary. For the sediment, the concentrations of Cr and Ni were above the limit established by CONAMA n° 454/2012 in the "City" site, and Cr above the TEL in all sampling sites. Ecotoxicological tests showed high toxicity in samples from "City" and "Tributary". The elements Cr, Mn, Ni and Zn were also higher in crabs from these sites. Cr levels exceeded the Brazilian limit for food consumption. The bioaccumulation factor was not significant. However, the overall analysis proved that this estuary is increasingly impacted by anthropogenic pressure.
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Affiliation(s)
- Anna Carolina de Freitas Santos da Silva
- State University of Feira de Santana (UEFS), Programa de Pós-Graduação em Modelagem em Ciências da Terra e do Ambiente (PPGM), Avenida Transnordestina, s/n - Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil.
| | - Carolina Oliveira de Santana
- State University of Feira de Santana (UEFS), Programa de Pós-Graduação em Ecologia e Evolução (PPGECOEVOL), Avenida Transnordestina, s/n - Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil
| | - Cristiane Dos Santos Vergilio
- Federal University of Espirito Santo (UFES), Laboratório de Ecotoxicologia, Departamento de Biologia, Centro de Ciências Exatas, Naturais e da Saúde, Alto Universitário, S/N, Guararema, 29.500-00 Alegre, Espírito Santo, Brazil
| | - Taíse Bomfim de Jesus
- State University of Feira de Santana (UEFS), Programa de Pós-Graduação em Modelagem em Ciências da Terra e do Ambiente (PPGM), Avenida Transnordestina, s/n - Novo Horizonte, 44036-900 Feira de Santana, Bahia, Brazil.
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4
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Wang X, Qu C, Miao J, Liu X, Yu Y, Leng K, Miao J. Transcriptome response of Antarctic Phaeodactylum tricornutum ICE-H producing dimethylsulphoniopropionate to hypersaline stress. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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5
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Noune F, Chaib N, Kaddeche H, Dzizi S, Metallaoui S, Blanco S. Effect of salinity on valves morphology in freshwater diatoms. Environ Monit Assess 2022; 195:159. [PMID: 36441291 DOI: 10.1007/s10661-022-10770-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Increased salt concentration is one of the most widespread problems affecting freshwater worldwide. Aquatic communities, and in particular periphytic diatoms, react to this alteration in water quality by modifying their structural parameters and physiology at the individual level, which is commonly manifested by the appearance of teratological forms. The present work presents the results of an experimental laboratory study in which a biofilm grown on artificial substrates was subjected to a gradient of water conductivities for 4 weeks. The results show an increase in the number of deformed valves over time proportionally to the increase in conductivity for each experimental treatment. These effects are also verified by analyzing the concentration of chlorophyll-a in the experimental biofilms, which demonstrate a metabolic response to the induced osmotic stress. No changes were recorded; however, in species richness or diversity of taxa present in the treatments. Our results, therefore, confirm at the experimental level numerous previous field observations about the harmful effect of salinity on periphytic diatoms, and also their ability to reintegrate with the new stress conditions.
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Affiliation(s)
- Faïza Noune
- Department of Natural and Life Sciences, Faculty of Sciences, University of 20 August 1955, Skikda, Algeria.
- Laboratoire de Recherche Sur La Physico-Chimie des Surfaces Et Interfaces (LRPCSI), University of 20 August 1955, Skikda, Algeria.
| | - Nadjla Chaib
- Department of Process Engineering, Faculty of Technology, University of 20 August 1955, Skikda, Algeria
- Laboratory of Catalysis, Bioprocesses and Environment - LCBE, University of 20 August 1955, Skikda, Algeria
| | - Hadjer Kaddeche
- Department of Natural and Life Sciences, Faculty of Sciences, University of 20 August 1955, Skikda, Algeria
- Laboratoire de Recherche Sur La Physico-Chimie des Surfaces Et Interfaces (LRPCSI), University of 20 August 1955, Skikda, Algeria
| | - Sabrina Dzizi
- Laboratoire de Recherche Sur La Physico-Chimie des Surfaces Et Interfaces (LRPCSI), University of 20 August 1955, Skikda, Algeria
- Department of Process Engineering, Faculty of Technology, University of 20 August 1955, Skikda, Algeria
| | - Sophia Metallaoui
- Department of Natural and Life Sciences, Faculty of Sciences, University of 20 August 1955, Skikda, Algeria
- Laboratoire de Recherche des Interactions, Biodiversité, Ecosystèmes et Biotechnologie (LRIBEB), University of 20 August 1955, Skikda, Algeria
| | - Saùl Blanco
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, Campus de Vegazana S/N, 24071, León, Spain
- Laboratorio de Diatomología, La Serna 58, 24007, León, Spain
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6
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Ma X, Johnson KB, Gu B, Zhang H, Li G, Huang X, Xia X. The in-situ release of algal bloom populations and the role of prokaryotic communities in their establishment and growth. Water Res 2022; 219:118565. [PMID: 35597219 DOI: 10.1016/j.watres.2022.118565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Harmful algal blooms (HABs) may quickly travel and inoculate new water bodies via currents and runoff in estuaries. The role of in-situ prokaryotic communities in the re-establishment and growth of inoculated algal blooms remains unknown. A novel on-board incubation experiment was employed to simulate the sudden surge of algal blooms to new estuarine waters and reveal possible outcomes. A dinoflagellate (Amphidinium carterae) and a diatom species (Thalassiosira weissflogii) which had bloomed in the Pearl River Estuary (PRE) area were cultured to bloom densities and reintroduced back into PRE natural seawaters. The diatom showed better adaptation ability to the new environment and increased significantly after the incubation. Simultaneously, particle-attached (PA) prokaryotic community structure was strongly influenced by adding of the diatom, with some opportunistic prokaryotes significantly enhanced in the diatom treatment. Whereas the dinoflagellate population did not increase following incubation, and their PA prokaryotic community showed no significant differences relative to the control. Metagenomic analyzes revealed that labile carbohydrates and organic nitrogen produced by the diatom contributed to the surge of certain PA prokaryotes. Genomic properties of a bacteria strain, which is affiliated with genus GMD16E07 (Planctomycetaceae) and comprised up to 50% of PA prokaryotes in the diatom treatment, was described here for the first time. Notably, the association of Planctomycetaceae and T. weissflogii likely represents symbiotic mutualism, with the diatom providing organic matter for Planctomycetaceae and the bacteria supplying vitamins and detoxifying nitriles and hydrogen peroxides in exchange. Therefore, the close association between Planctomycetaceae and T. weissflogii promoted the growth of both populations, and eventually facilitated the diatom bloom establishment.
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Affiliation(s)
- Xiao Ma
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
| | - Kevin B Johnson
- Department of Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Bowei Gu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hao Zhang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China.
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7
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Shaw DK, Sekar J, Ramalingam PV. Recent insights into oceanic dimethylsulfoniopropionate biosynthesis and catabolism. Environ Microbiol 2022; 24:2669-2700. [PMID: 35611751 DOI: 10.1111/1462-2920.16045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/29/2022]
Abstract
Dimethylsulfoniopropionate (DMSP), a globally important organosulfur compound is produced in prodigious amounts (2.0 Pg sulfur) annually in the marine environment by phytoplankton, macroalgae, heterotrophic bacteria, some corals and certain higher plants. It is an important marine osmolyte and a major precursor molecule for the production of climate-active volatile gas dimethyl sulfide (DMS). DMSP synthesis take place via three pathways: a transamination 'pathway-' in some marine bacteria and algae, a Met-methylation 'pathway-' in angiosperms and bacteria and a decarboxylation 'pathway-' in the dinoflagellate, Crypthecodinium. The enzymes DSYB and TpMMT are involved in the DMSP biosynthesis in eukaryotes while marine heterotrophic bacteria engage key enzymes such as DsyB and MmtN. Several marine bacterial communities import DMSP and degrade it via cleavage or demethylation pathways or oxidation pathway, thereby generating DMS, methanethiol, and dimethylsulfoxonium propionate, respectively. DMSP is cleaved through diverse DMSP lyase enzymes in bacteria and via Alma1 enzyme in phytoplankton. The demethylation pathway involves four different enzymes, namely DmdA, DmdB, DmdC and DmdD/AcuH. However, enzymes involved in the oxidation pathway have not been yet identified. We reviewed the recent advances on the synthesis and catabolism of DMSP and enzymes that are involved in these processes.
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Affiliation(s)
- Deepak Kumar Shaw
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Jegan Sekar
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Prabavathy Vaiyapuri Ramalingam
- Microbiology Lab, Department of Biotechnology, M. S. Swaminathan Research Foundation, Taramani, Chennai, 600113, Tamil Nadu, India
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8
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Shemi A, Alcolombri U, Schatz D, Farstey V, Vincent F, Rotkopf R, Ben-Dor S, Frada MJ, Tawfik DS, Vardi A. Dimethyl sulfide mediates microbial predator-prey interactions between zooplankton and algae in the ocean. Nat Microbiol 2021; 6:1357-1366. [PMID: 34697459 DOI: 10.1038/s41564-021-00971-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 09/01/2021] [Indexed: 12/11/2022]
Abstract
Phytoplankton are key components of the oceanic carbon and sulfur cycles1. During bloom events, some species can emit large amounts of the organosulfur volatile dimethyl sulfide (DMS) into the ocean and consequently the atmosphere, where it can modulate aerosol formation and affect climate2,3. In aquatic environments, DMS plays an important role as a chemical signal mediating diverse trophic interactions. Yet, its role in microbial predator-prey interactions remains elusive with contradicting evidence for its role in either algal chemical defence or in the chemo-attraction of grazers to prey cells4,5. Here we investigated the signalling role of DMS during zooplankton-algae interactions by genetic and biochemical manipulation of the algal DMS-generating enzyme dimethylsulfoniopropionate lyase (DL) in the bloom-forming alga Emiliania huxleyi6. We inhibited DL activity in E. huxleyi cells in vivo using the selective DL-inhibitor 2-bromo-3-(dimethylsulfonio)-propionate7 and overexpressed the DL-encoding gene in the model diatom Thalassiosira pseudonana. We showed that algal DL activity did not serve as an anti-grazing chemical defence but paradoxically enhanced predation by the grazer Oxyrrhis marina and other microzooplankton and mesozooplankton, including ciliates and copepods. Consumption of algal prey with induced DL activity also promoted O. marina growth. Overall, our results demonstrate that DMS-mediated grazing may be ecologically important and prevalent during prey-predator dynamics in aquatic ecosystems. The role of algal DMS revealed here, acting as an eat-me signal for grazers, raises fundamental questions regarding the retention of its biosynthetic enzyme through the evolution of dominant bloom-forming phytoplankton in the ocean.
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Affiliation(s)
- Adva Shemi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Alcolombri
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.,Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Daniella Schatz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Viviana Farstey
- The Inter-University Institute for Marine Sciences, Eilat, Israel
| | - Flora Vincent
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Miguel J Frada
- The Inter-University Institute for Marine Sciences, Eilat, Israel.,Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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9
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Cheng H, Shao Z, Lu C, Duan D. Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses. BMC Plant Biol 2021; 21:87. [PMID: 33568068 PMCID: PMC7874618 DOI: 10.1186/s12870-021-02849-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. RESULTS Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. CONCLUSIONS Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.
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Affiliation(s)
- Haomiao Cheng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhanru Shao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
| | - Chang Lu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co Ltd, Qingdao, 266400, P. R. China.
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10
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Thangaraj S, Palanisamy SK, Zhang G, Sun J. Quantitative Proteomic Profiling of Marine Diatom Skeletonema dohrnii in Response to Temperature and Silicate Induced Environmental Stress. Front Microbiol 2021; 11:554832. [PMID: 33519723 PMCID: PMC7841394 DOI: 10.3389/fmicb.2020.554832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Global warming is expected to reduce the nutrient concentration in the upper ocean and affect the physiology of marine diatoms, but the underlying molecular mechanisms controlling these physiological changes are currently unknown. To understand these mechanisms, here we investigated iTRAQ based proteomic profiling of diatom Skeletonema dohrnii in a multifactorial experimental with a combining change of temperature and silicate concentrations. In total, 3369 differently abundant proteins were detected in four different environmental conditions, and the function of all proteins was identified using Gene Ontology and KEGG pathway analysis. For discriminating the proteome variation among samples, multivariate statistical analysis (PCA, PLS-DA) was performed by comparing the protein ratio differences. Further, performing pathway analysis on diatom proteomes, we here demonstrated downregulation of photosynthesis, carbon metabolism, and ribosome biogenesis in the cellular process that leads to decrease the oxidoreductase activity and affects the cell cycle of the diatom. Using PLS-DA VIP score plot analysis, we identified 15 protein biomarkers for discriminating studied samples. Of these, five proteins or gene (rbcL, PRK, atpB, DNA-binding, and signal transduction) identified as key biomarkers, induced by temperature and silicate stress in diatom metabolism. Our results show that proteomic finger-printing of S. dohrnii with different environmental conditions adds biological information that strengthens marine phytoplankton proteome analysis.
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Affiliation(s)
| | - Satheesh Kumar Palanisamy
- Department of Zoology, School of Natural Science, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Guicheng Zhang
- Research Center for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, China
| | - Jun Sun
- College of Marine Science and Technology, China University of Geosciences, Wuhan, China
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11
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Nakov T, Judy KJ, Downey KM, Ruck EC, Alverson AJ. Transcriptional Response of Osmolyte Synthetic Pathways and Membrane Transporters in a Euryhaline Diatom During Long-term Acclimation to a Salinity Gradient. J Phycol 2020; 56:1712-1728. [PMID: 32750159 DOI: 10.1111/jpy.13061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 06/10/2020] [Indexed: 05/15/2023]
Abstract
How diatoms respond to fluctuations in osmotic pressure is important from both ecological and applied perspectives. It is well known that osmotic stress affects photosynthesis and can result in the accumulation of compounds desirable in pharmaceutical and alternative fuel industries. Gene expression responses to osmotic stress have been studied in short-term trials, but it is unclear whether the same mechanisms are recruited during long-term acclimation. We used RNA-seq to study the genome-wide transcription patterns in the euryhaline diatom, Cyclotella cryptica, following long-term acclimation to salinity that spanned the natural range of fresh to oceanic water. Long-term acclimated C. cryptica exhibited induced synthesis or repressed degradation of the osmolytes glycine betaine, taurine and dimethylsulfoniopropionate (DMSP). Although changes in proline concentration is one of the main responses in short-term osmotic stress, we did not detect a transcriptional change in proline biosynthetic pathways in our long-term experiment. Expression of membrane transporters showed a general tendency for increased import of potassium and export of sodium, consistent with the electrochemical gradients and dependence on co-transported molecules. Our results show substantial between-genotype differences in growth and gene expression reaction norms and suggest that the regulation of proline synthesis important in short-term osmotic stress might not be maintained in long-term acclimation. Further examination using time-course gene expression experiments, metabolomics and genetic validation of gene functions would reinforce patterns inferred from RNA-seq data.
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Affiliation(s)
- Teofil Nakov
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kathryn J Judy
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701, USA
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12
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Kumar G, Shekh A, Jakhu S, Sharma Y, Kapoor R, Sharma TR. Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application. Front Bioeng Biotechnol 2020; 8:914. [PMID: 33014997 PMCID: PMC7494788 DOI: 10.3389/fbioe.2020.00914] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 01/14/2023] Open
Abstract
Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.
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Affiliation(s)
- Gulshan Kumar
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ajam Shekh
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru, India
| | - Sunaina Jakhu
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Yogesh Sharma
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ritu Kapoor
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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13
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Ruprecht JE, Glamore WC, Dafforn KA, Wemheuer F, Crane SL, van Dorst J, Johnston EL, Mitrovic SM, Turner IL, Ferrari BC, Birrer SC. A novel real-world ecotoxicological dataset of pelagic microbial community responses to wastewater. Sci Data 2020; 7:158. [PMID: 32461582 PMCID: PMC7253417 DOI: 10.1038/s41597-020-0496-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/20/2020] [Indexed: 11/08/2022] Open
Abstract
Real-world observational datasets that record and quantify pressure-stressor-response linkages between effluent discharges and natural aquatic systems are rare. With global wastewater volumes increasing at unprecedented rates, it is urgent that the present dataset is available to provide the necessary information about microbial community structure and functioning. Field studies were performed at two time-points in the Austral summer. Single-species and microbial community whole effluent toxicity (WET) testing was performed at a complete range of effluent concentrations and two salinities, with accompanying environmental data to provide new insights into nutrient and organic matter cycling, and to identify ecotoxicological tipping points. The two salinity regimes were chosen to investigate future scenarios based on a predicted salinity increase at the study site, typical of coastal regions with rising sea levels globally. Flow cytometry, amplicon sequencing of 16S and 18S rRNA genes and micro-fluidic quantitative polymerase-chain reactions (MFQPCR) were used to determine chlorophyll-a and total bacterial cell numbers and size, as well as taxonomic and functional diversity of pelagic microbial communities. This strong pilot dataset could be replicated in other regions globally and would be of high value to scientists and engineers to support the next advances in microbial ecotoxicology, environmental biomonitoring and estuarine water quality modelling.
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Affiliation(s)
- J E Ruprecht
- Water Research Laboratory, School of Civil & Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - W C Glamore
- Water Research Laboratory, School of Civil & Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - K A Dafforn
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
- Department of Earth and Environmental Sciences, Macquarie University, Macquarie Park, NSW, 2109, Australia
| | - F Wemheuer
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - S L Crane
- Ferrari Lab, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - J van Dorst
- Ferrari Lab, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - E L Johnston
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - S M Mitrovic
- Freshwater and Estuarine Research Group, School of Life Sciences, University of Technology Sydney, Ultimo, 2007, NSW, Australia
| | - I L Turner
- Water Research Laboratory, School of Civil & Environmental Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - B C Ferrari
- Ferrari Lab, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - S C Birrer
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
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14
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McParland EL, Wright A, Art K, He M, Levine NM. Evidence for contrasting roles of dimethylsulfoniopropionate production in Emiliania huxleyi and Thalassiosira oceanica. New Phytol 2020; 226:396-409. [PMID: 31850524 PMCID: PMC7154784 DOI: 10.1111/nph.16374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/27/2019] [Indexed: 05/28/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a globally abundant marine metabolite and a significant source of organic carbon and sulfur for marine microbial ecosystems with the potential to influence climate regulation. However, the physiological function of DMSP has remained enigmatic for >30 yr. Recent insight suggests that there are different physiological roles for DMSP based on the cellular DMSP concentrations in producers. Differential production of DMSP was tested with multiple physiological experiments that altered nitrate availability, salinity and temperature to create stressed growth and target different metabolic conditions in Emiliania huxleyi, a high DMSP producer and Thalassiosira oceanica, a low DMSP producer. Emiliania huxleyi intracellular DMSP did not respond to metabolically imbalanced conditions, while Thalassiosira oceanica intracellular DMSP was significantly correlated to stressed growth rate across all conditions tested and exhibited a plastic response on a timescale of hours in nonsteady-state. The previous assumption that proposed DMSP mechanism(s) can be universally applied to all producers is shown to be unlikely. Rather, two distinct ecological roles for DMSP likely exist that differ by producer type, where: (1) the primary role of DMSP in high producers is a constitutive compatible solute; and (2) DMSP production in low producers is a finely tuned stress response.
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Affiliation(s)
- Erin L. McParland
- Department of Marine Chemistry and GeochemistryWoods Hole Oceanographic InstitutionWoods HoleMA02543USA
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
| | - Anna Wright
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
| | - Kristin Art
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
| | - Meagan He
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
| | - Naomi M. Levine
- Department of Marine and Environmental BiologyUniversity of Southern CaliforniaLos AngelesCA90089USA
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15
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Gwinn JK, Robertson A, Kiene RP. Effect of Salinity on DMSP Production in Gambierdiscus belizeanus (Dinophyceae). J Phycol 2019; 55:1401-1411. [PMID: 31523812 DOI: 10.1111/jpy.12923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is produced by many species of marine phytoplankton and has been reported to provide a variety of beneficial functions including osmoregulation. Dinoflagellates are recognized as major DMSP producers; however, accumulation has been shown to be highly variable in this group. We explored the effect of hyposaline transfer in Gambierdiscus belizeanus between ecologically relevant salinities (36 and 31) on DMSP accumulation, Chl a, cell growth, and cell volume, over 12 d. Our results showed that G. belizeanus maintained an intracellular DMSP content of 16.3 pmol cell-1 and concentration of 139 mM in both salinities. Although this intracellular concentration was near the median reported for other dinoflagellates, the cellular content achieved by G. belizeanus was the highest reported of any dinoflagellate thus far, owing mainly to its large size. DMSP levels were not significantly affected by salinity treatment but did change over time during the experiment. Salinity, however, did have a significant effect on the ratio of DMSP:Chl a, suggesting that salinity transfer of G. belizeanus induced a physiological response other than DMSP adjustment. A survey of DMSP content in a variety of Gambierdiscus species and strains revealed relatively high DMSP concentrations (1.0-16.4 pmol cell-1 ) as well as high intrageneric and intraspecific variation. We conclude that, although DMSP may not be involved in long-term (3-12 d) osmoregulation in this species, G. belizeanus and other Gambierdiscus species may be important contributors to DMSP production in tropical benthic microalgal communities due to their large size and high cellular content.
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Affiliation(s)
- Jessica K Gwinn
- Department of Marine Sciences, University of South Alabama, Mobile, Alabama, 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, Alabama, 36528, USA
| | - Alison Robertson
- Department of Marine Sciences, University of South Alabama, Mobile, Alabama, 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, Alabama, 36528, USA
| | - Ronald P Kiene
- Department of Marine Sciences, University of South Alabama, Mobile, Alabama, 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, Alabama, 36528, USA
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16
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Zhang XH, Liu J, Liu J, Yang G, Xue CX, Curson ARJ, Todd JD. Biogenic production of DMSP and its degradation to DMS-their roles in the global sulfur cycle. Sci China Life Sci 2019; 62:1296-1319. [PMID: 31231779 DOI: 10.1007/s11427-018-9524-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/16/2019] [Indexed: 01/08/2023]
Abstract
Dimethyl sulfide (DMS) is the most abundant form of volatile sulfur in Earth's oceans, and is mainly produced by the enzymatic clevage of dimethylsulfoniopropionate (DMSP). DMS and DMSP play important roles in driving the global sulfur cycle and may affect climate. DMSP is proposed to serve as an osmolyte, a grazing deterrent, a signaling molecule, an antioxidant, a cryoprotectant and/or as a sink for excess sulfur. It was long believed that only marine eukaryotes such as phytoplankton produce DMSP. However, we recently discovered that marine heterotrophic bacteria can also produce DMSP, making them a potentially important source of DMSP. At present, one prokaryotic and two eukaryotic DMSP synthesis enzymes have been identified. Marine heterotrophic bacteria are likely the major degraders of DMSP, using two known pathways: demethylation and cleavage. Many phytoplankton and some fungi can also cleave DMSP. So far seven different prokaryotic and one eukaryotic DMSP lyases have been identified. This review describes the global distribution pattern of DMSP and DMS, the known genes for biosynthesis and cleavage of DMSP, and the physiological and ecological functions of these important organosulfur molecules, which will improve understanding of the mechanisms of DMSP and DMS production and their roles in the environment.
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Affiliation(s)
- Xiao-Hua Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Ji Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jingli Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Guipeng Yang
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao, 266071, China
| | - Chun-Xu Xue
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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17
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Heal KR, Kellogg NA, Carlson LT, Lionheart RM, Ingalls AE. Metabolic Consequences of Cobalamin Scarcity in the Diatom Thalassiosira pseudonana as Revealed Through Metabolomics. Protist 2019; 170:328-348. [PMID: 31260945 DOI: 10.1016/j.protis.2019.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 05/17/2019] [Accepted: 05/19/2019] [Indexed: 02/07/2023]
Abstract
Diatoms perform an estimated 20% of global photosynthesis, form the base of the marine food web, and sequester carbon into the deep ocean through the biological pump. In some areas of the ocean, diatom growth is limited by the micronutrient cobalamin (vitamin B12), yet the biochemical ramifications of cobalamin limitation are not well understood. In a laboratory setting, we grew the diatom Thalassiosira pseudonana under replete and low cobalamin conditions to elucidate changes in metabolite pools. Using metabolomics, we show that the diatom experienced a metabolic cascade under cobalamin limitation that affected the central methionine cycle, transsulfuration pathway, and composition of osmolyte pools. In T. pseudonana, 5'-methylthioadenosine decreased under low cobalamin conditions, suggesting a disruption in the diatom's polyamine biosynthesis. Furthermore, two acylcarnitines accumulated under low cobalamin, suggesting the limited use of an adenosylcobalamin-dependent enzyme, methylmalonyl CoA mutase. Overall, these changes in metabolite pools yield insight into the metabolic consequences of cobalamin limitation in diatoms and suggest that cobalamin availability may have consequences for microbial interactions that are based on metabolite production by phytoplankton.
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Affiliation(s)
- Katherine R Heal
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Natalie A Kellogg
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Laura T Carlson
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Regina M Lionheart
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Anitra E Ingalls
- School of Oceanography, University of Washington, Seattle, WA 98195, USA.
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18
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Nelson DR, Chaiboonchoe A, Fu W, Hazzouri KM, Huang Z, Jaiswal A, Daakour S, Mystikou A, Arnoux M, Sultana M, Salehi-Ashtiani K. Potential for Heightened Sulfur-Metabolic Capacity in Coastal Subtropical Microalgae. iScience 2019; 11:450-465. [PMID: 30684492 PMCID: PMC6348204 DOI: 10.1016/j.isci.2018.12.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/07/2018] [Accepted: 12/28/2018] [Indexed: 12/05/2022] Open
Abstract
The activities of microalgae support nutrient cycling that helps to sustain aquatic and terrestrial ecosystems. Most microalgal species, especially those from the subtropics, are genomically uncharacterized. Here we report the isolation and genomic characterization of 22 microalgal species from subtropical coastal regions belonging to multiple clades and three from temperate areas. Halotolerant strains including Halamphora, Dunaliella, Nannochloris, and Chloroidium comprised the majority of these isolates. The subtropical-based microalgae contained arrays of methyltransferase, pyridine nucleotide-disulfide oxidoreductase, abhydrolase, cystathionine synthase, and small-molecule transporter domains present at high relative abundance. We found that genes for sulfate transport, sulfotransferase, and glutathione S-transferase activities were especially abundant in subtropical, coastal microalgal species and halophytic species in general. Our metabolomics analyses indicate lineage- and habitat-specific sets of biomolecules implicated in niche-specific biological processes. This work effectively expands the collection of available microalgal genomes by ∼50%, and the generated resources provide perspectives for studying halophyte adaptive traits. We have sequenced 20+ microallgal genomes from the subtropics This new collection increases the available microalgal genomes by ∼50% Metabolomics indicates lineage- and habitat-specificity of biomolecules Coastal, subtropical species of microalgae show expansion of sulfur-metabolic genes
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Affiliation(s)
- David R Nelson
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Weiqi Fu
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Khaled M Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, Al-Ain, UAE
| | - Ziyuan Huang
- Department of Computer Science, New York University Shanghai, Shanghai, China
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Alexandra Mystikou
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Marc Arnoux
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Mehar Sultana
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
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19
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Carnat G, Said-Ahmad W, Fripiat F, Wittek B, Tison JL, Uhlig C, Amrani A. Variability in sulfur isotope composition suggests unique dimethylsulfoniopropionate cycling and microalgae metabolism in Antarctic sea ice. Commun Biol 2018; 1:212. [PMID: 30534604 DOI: 10.1038/s42003-018-0228-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/13/2018] [Indexed: 11/08/2022] Open
Abstract
Sea ice microbial communities produce large amounts of the sulfur metabolite dimethylsulfoniopropionate (DMSP), a precursor of the climate cooling gas dimethylsulfide. Despite their importance to the polar sulfur cycle, drivers and metabolic pathways of sea ice DMSP are uncertain. Here we report the first measurements of sea ice DMSP sulfur isotopic composition (34S/32S ratio, δ34S). δ34S values in ice cores from the Ross Sea and Weddell Sea reveal considerable variability across seasons and between ice horizons (from +10.6 to +23.6‰). We discuss how the most extreme δ34S values observed could be related to unique DMSP cycling in the seasonally extreme physiochemical conditions of isolated brine inclusions in winter-spring. Using cell cultures, we show that part of the DMSP δ34S variability could be explained by distinct DMSP metabolism in sea ice microalgae. These findings advance our understanding of the sea ice sulfur cycle and metabolic adaptations of microbes in extreme environments.
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Richter LV, Mansfeldt CB, Kuan MM, Cesare AE, Menefee ST, Richardson RE, Ahner BA. Altered Microbiome Leads to Significant Phenotypic and Transcriptomic Differences in a Lipid Accumulating Chlorophyte. Environ Sci Technol 2018; 52:6854-6863. [PMID: 29750518 DOI: 10.1021/acs.est.7b06581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Given the challenges facing the economically favorable production of products from microalgae, understanding factors that might impact productivity rates including growth rates and accumulation of desired products, for example, triacylglycerols (TAG) for biodiesel feedstock, remains critical. Although operational parameters such as media composition and reactor design can clearly effect growth rates, the role of microbe-microbe interactions is just beginning to be elucidated. In this study an oleaginous marine algae Chlorella spp. C596 culture is shown to be better described as a microbial community. Perturbations to this microbial community showed a significant impact on phenotypes including sustained differences in growth rate and TAG accumulation of 2.4 and 2.5 fold, respectively. Characterization of the associated community using Illumina 16S rRNA amplicon and random shotgun transcriptomic analyses showed that the fast growth rate correlated with two specific bacterial species ( Ruegeria and Rhodobacter spp). The transcriptomic response of the Chlorella species revealed that the slower growing algal consortium C596-S1 upregulated genes associated with photosynthesis and resource scavenging and decreased the expression of genes associated with transcription and translation relative to the initial C596-R1. Our studies advance the appreciation of the effects microbiomes can have on algal growth in bioreactors and suggest that symbiotic interactions are involved in a range of critical processes including nitrogen, carbon cycling, and oxidative stress.
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Affiliation(s)
- Lubna V Richter
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Cresten B Mansfeldt
- School of Civil and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Michael M Kuan
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Alexandra E Cesare
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Stephen T Menefee
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Ruth E Richardson
- School of Civil and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Beth A Ahner
- Department of Biological and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
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22
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Kageyama H, Tanaka Y, Shibata A, Waditee-Sirisattha R, Takabe T. Dimethylsulfoniopropionate biosynthesis in a diatom Thalassiosira pseudonana: Identification of a gene encoding MTHB-methyltransferase. Arch Biochem Biophys 2018; 645:100-106. [PMID: 29574051 DOI: 10.1016/j.abb.2018.03.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/16/2018] [Accepted: 03/17/2018] [Indexed: 10/17/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is one of the most abundant molecules on earth and plays a pivotal role in the marine sulfur cycle. DMSP is believed to be synthesized from methionine by a four-step reaction pathway in marine algae. The genes responsible for biosynthesis of DMSP remain unidentified. A diatom Thalassiosira pseudonana CCMP1335 is an important component of marine ecosystems and contributes greatly to the world's primary production. In this study, through genome search, in vivo activity and functional studies of cDNA products, a gene encoding Thalassiosira methyltransferase (TpMMT) which catalyzes the key step of DMSP synthesis formation of 4-methylthio-2-hydroxybutyrate (DMSHB) from 4-methylthio-2-oxobutyrate (MTHB), was identified. The amino acid sequence of TpMMT was homologous to the methyltransferase from Phaeodactylum tricornutum CCAP 1055/1, but not the recently identified bacterium gene. High salinity and nitrogen limitation stresses caused the increase of DMSP content and TpMMT protein in Thalassiosira. In addition to TpMMT, the enzyme activities for the first three steps could be detected and enhanced under high salinity, suggesting the importance of four-step DMSP synthetic pathway in Thalassiosira.
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Affiliation(s)
- Hakuto Kageyama
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya 468-8502, Japan
| | - Yoshito Tanaka
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya 468-8502, Japan
| | - Ayumi Shibata
- Research Institute, Meijo University, Nagoya 468-8502, Japan
| | | | - Teruhiro Takabe
- Graduate School of Environmental and Human Sciences, Meijo University, Nagoya 468-8502, Japan; Research Institute, Meijo University, Nagoya 468-8502, Japan.
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23
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Curson ARJ, Williams BT, Pinchbeck BJ, Sims LP, Martínez AB, Rivera PPL, Kumaresan D, Mercadé E, Spurgin LG, Carrión O, Moxon S, Cattolico RA, Kuzhiumparambil U, Guagliardo P, Clode PL, Raina JB, Todd JD. DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton. Nat Microbiol 2018; 3:430-439. [PMID: 29483657 DOI: 10.1038/s41564-018-0119-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/29/2018] [Indexed: 01/08/2023]
Abstract
Dimethylsulfoniopropionate (DMSP) is a globally important organosulfur molecule and the major precursor for dimethyl sulfide. These compounds are important info-chemicals, key nutrients for marine microorganisms, and are involved in global sulfur cycling, atmospheric chemistry and cloud formation1-3. DMSP production was thought to be confined to eukaryotes, but heterotrophic bacteria can also produce DMSP through the pathway used by most phytoplankton 4 , and the DsyB enzyme catalysing the key step of this pathway in bacteria was recently identified 5 . However, eukaryotic phytoplankton probably produce most of Earth's DMSP, yet no DMSP biosynthesis genes have been identified in any such organisms. Here we identify functional dsyB homologues, termed DSYB, in many phytoplankton and corals. DSYB is a methylthiohydroxybutryate methyltransferase enzyme localized in the chloroplasts and mitochondria of the haptophyte Prymnesium parvum, and stable isotope tracking experiments support these organelles as sites of DMSP synthesis. DSYB transcription levels increased with DMSP concentrations in different phytoplankton and were indicative of intracellular DMSP. Identification of the eukaryotic DSYB sequences, along with bacterial dsyB, provides the first molecular tools to predict the relative contributions of eukaryotes and prokaryotes to global DMSP production. Furthermore, evolutionary analysis suggests that eukaryotic DSYB originated in bacteria and was passed to eukaryotes early in their evolution.
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Affiliation(s)
- Andrew R J Curson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | - Leanne P Sims
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | | | - Deepak Kumaresan
- School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Elena Mercadé
- Laboratory of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ornella Carrión
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | | | | | - Paul Guagliardo
- The Centre for Microscopy Characterisation and Analysis, University of Western Australia, Crawley, Australia
| | - Peta L Clode
- The Centre for Microscopy Characterisation and Analysis, University of Western Australia, Crawley, Australia.,Oceans Institute, University of Western Australia, Crawley, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster (C3), Faculty of Science, University of Technology, Sydney, New South Wales, Australia
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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24
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Aguilar C, Raina JB, Motti CA, Fôret S, Hayward DC, Lapeyre B, Bourne DG, Miller DJ. Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals. BMC Genomics 2017; 18:612. [PMID: 28806970 PMCID: PMC5557254 DOI: 10.1186/s12864-017-3959-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/25/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dimethylsulfoniopropionate (DMSP) is a small sulphur compound which is produced in prodigious amounts in the oceans and plays a pivotal role in the marine sulfur cycle. Until recently, DMSP was believed to be synthesized exclusively by photosynthetic organisms; however we now know that corals and specific bacteria can also produce this compound. Corals are major sources of DMSP, but the molecular basis for its biosynthesis is unknown in these organisms. RESULTS Here we used salinity stress, which is known to trigger DMSP production in other organisms, in conjunction with transcriptomics to identify coral genes likely to be involved in DMSP biosynthesis. We focused specifically on both adults and juveniles of the coral Acropora millepora: after 24 h of exposure to hyposaline conditions, DMSP concentrations increased significantly by 2.6 fold in adult corals and 1.2 fold in juveniles. Concomitantly, candidate genes enabling each of the necessary steps leading to DMSP production were up-regulated. CONCLUSIONS The data presented strongly suggest that corals use an algal-like pathway to generate DMSP from methionine, and are able to rapidly change expression of the corresponding genes in response to environmental stress. However, our data also indicate that DMSP is unlikely to function primarily as an osmolyte in corals, instead potentially serving as a scavenger of ROS and as a molecular sink for excess methionine produced as a consequence of proteolysis and osmolyte catabolism in corals under hypo-osmotic conditions.
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Affiliation(s)
- Catalina Aguilar
- AIMS@JCU, and Department of Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia
| | - Jean-Baptiste Raina
- Climate Change Cluster (C3), Faculty of Science, University of Technology, Sydney, NSW, 2007, Australia
| | - Cherie A Motti
- Australian Institute of Marine Science, Townsville, 4810, Queensland, Australia
| | - Sylvain Fôret
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia.,Evolution and Ecology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - David C Hayward
- Evolution and Ecology, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Bruno Lapeyre
- Laboratoire d'excellence CORAIL, Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), Moorea, B.P. 1013, Papeete, French Polynesia
| | - David G Bourne
- AIMS@JCU, and Department of Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia. .,Australian Institute of Marine Science, Townsville, 4810, Queensland, Australia. .,College of Science and Engineering, James Cook University, Townsville, 4811, Queensland, Australia.
| | - David J Miller
- AIMS@JCU, and Department of Molecular and Cell Biology, James Cook University, Townsville, 4811, Queensland, Australia. .,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, 4811, Queensland, Australia.
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25
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Dani KGS, Loreto F. Trade-Off Between Dimethyl Sulfide and Isoprene Emissions from Marine Phytoplankton. Trends Plant Sci 2017; 22:361-372. [PMID: 28242195 DOI: 10.1016/j.tplants.2017.01.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/04/2017] [Accepted: 01/24/2017] [Indexed: 05/14/2023]
Abstract
Marine phytoplankton emit volatile organic compounds (VOCs) such as dimethyl sulfide (DMS) and isoprene that influence air quality, cloud dynamics, and planetary albedo. We show that globally (i) marine phytoplankton taxa tend to emit either DMS or isoprene, and (ii) sea-water surface concentration and emission hotspots of DMS and isoprene have opposite latitudinal gradients. We argue that a convergence of antioxidant functions between DMS and isoprene is possible, driven by potential metabolic competition for photosynthetic substrates. Linking phytoplankton emission traits to their latitudinal niches, we hypothesize that natural selection favors DMS emission in cold (polar) waters and isoprene emission in warm (tropical) oceans, and that global warming may expand the geographic range of marine isoprene-emitters. A trade-off between DMS and isoprene at metabolic, organismal, and geographic levels may have important consequences for future marine biosphere-atmosphere interactions.
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Affiliation(s)
- K G Srikanta Dani
- Istituto per lo Studio degli Ecosistemi, Consiglio Nazionale delle Ricerche, Via Madonna del Piano 10, Sesto Fiorentino, 50019 Firenze, Italy; School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695016 Kerala, India.
| | - Francesco Loreto
- Dipartimento di Scienze Bio-Agroalimentari, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro 7, 00185 Roma, Italy.
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26
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Bullock HA, Luo H, Whitman WB. Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria. Front Microbiol 2017; 8:637. [PMID: 28469605 PMCID: PMC5395565 DOI: 10.3389/fmicb.2017.00637] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 03/28/2017] [Indexed: 11/13/2022] Open
Abstract
The elucidation of the pathways for dimethylsulfoniopropionate (DMSP) synthesis and metabolism and the ecological impact of DMSP have been studied for nearly 70 years. Much of this interest stems from the fact that DMSP metabolism produces the climatically active gas dimethyl sulfide (DMS), the primary natural source of sulfur to the atmosphere. DMSP plays many important roles for marine life, including use as an osmolyte, antioxidant, predator deterrent, and cryoprotectant for phytoplankton and as a reduced carbon and sulfur source for marine bacteria. DMSP is hypothesized to have become abundant in oceans approximately 250 million years ago with the diversification of the strong DMSP producers, the dinoflagellates. This event coincides with the first genome expansion of the Roseobacter clade, known DMSP degraders. Structural and mechanistic studies of the enzymes of the bacterial DMSP demethylation and cleavage pathways suggest that exposure to DMSP led to the recruitment of enzymes from preexisting metabolic pathways. In some cases, such as DmdA, DmdD, and DddP, these enzymes appear to have evolved to become more specific for DMSP metabolism. By contrast, many of the other enzymes, DmdB, DmdC, and the acrylate utilization hydratase AcuH, have maintained broad functionality and substrate specificities, allowing them to carry out a range of reactions within the cell. This review will cover the experimental evidence supporting the hypothesis that, as DMSP became more readily available in the marine environment, marine bacteria adapted enzymes already encoded in their genomes to utilize this new compound.
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Affiliation(s)
- Hannah A Bullock
- Department of Microbiology, University of Georgia, AthensGA, USA
| | - Haiwei Luo
- School of Life Sciences, The Chinese University of Hong KongHong Kong, Hong Kong
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27
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Sang W, Huang ZR, Yang LT, Guo P, Ye X, Chen LS. Effects of High Toxic Boron Concentration on Protein Profiles in Roots of Two Citrus Species Differing in Boron-Tolerance Revealed by a 2-DE Based MS Approach. Front Plant Sci 2017; 8:180. [PMID: 28261239 PMCID: PMC5313502 DOI: 10.3389/fpls.2017.00180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/30/2017] [Indexed: 05/02/2023]
Abstract
Citrus are sensitive to boron (B)-toxicity. In China, B-toxicity occurs in some citrus orchards. So far, limited data are available on B-toxicity-responsive proteins in higher plants. Thirteen-week-old seedlings of "Sour pummelo" (Citrus grandis) and "Xuegan" (Citrus sinensis) was fertilized every other day until dripping with nutrient solution containing 10 μM (control) or 400 μM (B-toxicity) H3BO3 for 15 weeks. The typical B-toxic symptom only occurred in 400 μM B-treated C. grandis leaves, and that B-toxicity decreased root dry weight more in C. grandis seedlings than in C. sinensis ones, demonstrating that C. sinensis was more tolerant to B-toxicity than C. grandis. Using a 2-dimensional electrophoresis (2-DE) based MS approach, we identified 27 up- and four down-accumulated, and 28 up- and 13 down-accumulated proteins in B-toxic C. sinensis and C. grandis roots, respectively. Most of these proteins were isolated only from B-toxic C. sinensis or C. grandis roots, only nine B-toxicity-responsive proteins were shared by the two citrus species. Great differences existed in B-toxicity-induced alterations of protein profiles between C. sinensis and C. grandis roots. More proteins related to detoxification were up-accumulated in B-toxic C. grandis roots than in B-toxic C. sinensis roots to meet the increased requirement for the detoxification of the more reactive oxygen species and other toxic compounds such as aldehydes in the former. For the first time, we demonstrated that the active methyl cycle was induced and repressed in B-toxic C. sinensis and C. grandis roots, respectively, and that C. sinensis roots had a better capacity to keep cell wall and cytoskeleton integrity than C. grandis roots in response to B-toxicity, which might be responsible for the higher B-tolerance of C. sinensis. In addition, proteins involved in nucleic acid metabolism, biological regulation and signal transduction might play a role in the higher B-tolerance of C. sinensis.
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Affiliation(s)
- Wen Sang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
- College of Horticulture, Fujian Agriculture and Forestry UniversityFuzhou, China
- Agriculture, Forestry and Water Conservancy Bureau of Xinzhou DistrictShangrao, China
| | - Zeng-Rong Huang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Lin-Tong Yang
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Peng Guo
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xin Ye
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Li-Song Chen
- Institute of Plant Nutritional Physiology and Molecular Biology, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhou, China
- The Higher Educational Key Laboratory of Fujian Province for Soil Ecosystem Health and Regulation, Fujian Agriculture and Forestry UniversityFuzhou, China
- *Correspondence: Li-Song Chen
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28
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Longworth J, Wu D, Huete-Ortega M, Wright PC, Vaidyanathan S. Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion. ALGAL RES 2016; 18:213-224. [PMID: 27812494 PMCID: PMC5070409 DOI: 10.1016/j.algal.2016.06.015] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 05/08/2016] [Accepted: 06/14/2016] [Indexed: 11/26/2022]
Abstract
Nitrogen stress is a common strategy employed to stimulate lipid accumulation in microalgae, a biofuel feedstock of topical interest. Although widely investigated, the underlying mechanism of this strategy is still poorly understood. We examined the proteome response of lipid accumulation in the model diatom, Phaeodactylum tricornutum (CCAP 1055/1), at an earlier stage of exposure to selective nitrogen exclusion than previously investigated, and at a time point when changes would reflect lipid accumulation more than carbohydrate accumulation. In total 1043 proteins were confidently identified (≥ 2 unique peptides) with 645 significant (p < 0.05) changes observed, in the LC-MS/MS based iTRAQ investigation. Analysis of significant changes in KEGG pathways and individual proteins showed that under nitrogen starvation P. tricornutum reorganizes its proteome in favour of nitrogen scavenging and reduced lipid degradation whilst rearranging the central energy metabolism that deprioritizes photosynthetic pathways. By doing this, this species appears to increase nitrogen availability inside the cell and limit its use to the pathways where it is needed most. Compared to previously published proteomic analysis of nitrogen starvation in Chlamydomonas reinhardtii, central energy metabolism and photosynthesis appear to be affected more in the diatom, whilst the green algae appears to invest its energy in reorganizing respiration and the cellular organization pathways.
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29
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Bussard A, Corre E, Hubas C, Duvernois-Berthet E, Le Corguillé G, Jourdren L, Coulpier F, Claquin P, Lopez PJ. Physiological adjustments and transcriptome reprogramming are involved in the acclimation to salinity gradients in diatoms. Environ Microbiol 2016; 19:909-925. [DOI: 10.1111/1462-2920.13398] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrien Bussard
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
| | - Erwan Corre
- CNRS, UPMC, FR2424, ABiMS, Station Biologique; Roscoff 29680 France
| | - Cédric Hubas
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
| | | | | | - Laurent Jourdren
- Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Plateforme Génomique; Paris 75005 France
| | - Fanny Coulpier
- Ecole Normale Supérieure, PSL Research University, CNRS, Inserm, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Plateforme Génomique; Paris 75005 France
| | - Pascal Claquin
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA, Esplanade de la paix; Caen 14032 France
| | - Pascal Jean Lopez
- UMR Biologie des Organismes et des Ecosystèmes Aquatiques, CNRS 7208-MNHN-UPMC-IRD 207-UCN-UA; 43 rue Cuvier Paris 75005 France
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30
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Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PLoS One 2016; 11:e0155038. [PMID: 27152931 PMCID: PMC4859558 DOI: 10.1371/journal.pone.0155038] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/22/2016] [Indexed: 11/18/2022] Open
Abstract
Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.
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Affiliation(s)
- Jennifer Levering
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Jared Broddrick
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | | | - Graham Peers
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Karen Beeri
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Joshua Mayers
- Division of Industrial Biotechnology, Department of Biology and Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Alessandra A. Gallina
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Andrew E. Allen
- J. Craig Venter Institute, La Jolla, California, United States of America
- Integrative Oceanography Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
| | - Karsten Zengler
- Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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31
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Muhseen ZT, Xiong Q, Chen Z, Ge F. Proteomics studies on stress responses in diatoms. Proteomics 2015; 15:3943-53. [PMID: 26364674 DOI: 10.1002/pmic.201500165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/09/2015] [Accepted: 09/09/2015] [Indexed: 01/09/2023]
Abstract
Diatoms are a highly diverse group of eukaryotic phytoplankton that are distributed throughout marine and freshwater environments and are believed to be responsible for approximately 40% of the total marine primary productivity. The ecological success of diatoms suggests that they have developed a range of strategies to cope with various biotic and abiotic stress factors. It is of great interest to understand the adaptive responses of diatoms to different stresses in the marine environment. Proteomic technologies have been applied to the adaptive responses of marine diatoms under different growth conditions in recent years such as nitrogen starvation, iron limitation and phosphorus deficiency. These studies have provided clues to elucidate the sophisticated sensing mechanisms that control their adaptive responses. Although only a very limited number of proteomic studies were conducted in diatoms, the obtained data have led to a better understanding of the biochemical processes that contribute to their ecological success. This review presents the current status of proteomic studies of diatom stress responses and discusses the novel developments and applications for the analysis of protein post-translational modification in diatoms. The potential future application of proteomics could contribute to a better understanding of the physiological mechanisms underlying diatom acclimation to a given stress and the acquisition of an enhanced diatom stress tolerance. Future challenges and research opportunities in the proteomics studies of diatoms are also discussed.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
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