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Lauritano C, Montuori E, De Falco G, Carrella S. In Silico Methodologies to Improve Antioxidants' Characterization from Marine Organisms. Antioxidants (Basel) 2023; 12:710. [PMID: 36978958 PMCID: PMC10045275 DOI: 10.3390/antiox12030710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023] Open
Abstract
Marine organisms have been reported to be valuable sources of bioactive molecules that have found applications in different industrial fields. From organism sampling to the identification and bioactivity characterization of a specific compound, different steps are necessary, which are time- and cost-consuming. Thanks to the advent of the -omic era, numerous genome, metagenome, transcriptome, metatranscriptome, proteome and microbiome data have been reported and deposited in public databases. These advancements have been fundamental for the development of in silico strategies for basic and applied research. In silico studies represent a convenient and efficient approach to the bioactivity prediction of known and newly identified marine molecules, reducing the time and costs of "wet-lab" experiments. This review focuses on in silico approaches applied to bioactive molecule discoveries from marine organisms. When available, validation studies reporting a bioactivity assay to confirm the presence of an antioxidant molecule or enzyme are reported, as well. Overall, this review suggests that in silico approaches can offer a valuable alternative to most expensive approaches and proposes them as a little explored field in which to invest.
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Affiliation(s)
- Chiara Lauritano
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
| | - Eleonora Montuori
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres 31, 98166 Messina, Italy
| | - Gabriele De Falco
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
| | - Sabrina Carrella
- Ecosustainable Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, Via Acton 55, 80133 Napoli, Italy
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Ruocco M, Barrote I, Hofman JD, Pes K, Costa MM, Procaccini G, Silva J, Dattolo E. Daily Regulation of Key Metabolic Pathways in Two Seagrasses Under Natural Light Conditions. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.757187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The circadian clock is an endogenous time-keeping mechanism that enables organisms to adapt to external environmental cycles. It produces rhythms of plant metabolism and physiology, and interacts with signaling pathways controlling daily and seasonal environmental responses through gene expression regulation. Downstream metabolic outputs, such as photosynthesis and sugar metabolism, besides being affected by the clock, can also contribute to the circadian timing itself. In marine plants, studies of circadian rhythms are still way behind in respect to terrestrial species, which strongly limits the understanding of how they coordinate their physiology and energetic metabolism with environmental signals at sea. Here, we provided a first description of daily timing of key core clock components and clock output pathways in two seagrass species, Cymodocea nodosa and Zostera marina (order Alismatales), co-occurring at the same geographic location, thus exposed to identical natural variations in photoperiod. Large differences were observed between species in the daily timing of accumulation of transcripts related to key metabolic pathways, such as photosynthesis and sucrose synthesis/transport, highlighting the importance of intrinsic biological, and likely ecological attributes of the species in determining the periodicity of functions. The two species exhibited a differential sensitivity to light-to-dark and dark-to-light transition times and could adopt different growth timing based on a differential strategy of resource allocation and mobilization throughout the day, possibly coordinated by the circadian clock. This behavior could potentially derive from divergent evolutionary adaptations of the species to their bio-geographical range of distributions.
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Boutahar L, Espinosa F, Sempere-Valverde J, Selfati M, Bazairi H. Trace element bioaccumulation in the seagrass Cymodocea nodosa from a polluted coastal lagoon: Biomonitoring implications. MARINE POLLUTION BULLETIN 2021; 166:112209. [PMID: 33714036 DOI: 10.1016/j.marpolbul.2021.112209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
This is the first investigation of the potential for using Cymodocea nodosa to biomonitor trace element (TE) contamination in Marchica lagoon (Morocco), a Mediterranean pollution hotspot. We measured concentrations of seven TEs in seagrass tissues (leaf-rhizome-root) and sediments. Single and multi-element indices confirmed that sediments near illegal discharges were heavily polluted and we predicted risks of frequent adverse biological effects in these areas. Four of the TEs increased concentrations in C. nodosa leaf and root along sediment pollution gradient. Leaves and roots were both good indicators of Cu and Cd contamination in sediment, whereas leaves were the best indicator of Zn and roots for Pb. This seagrass was not a bioindicator of Al, Cr and Ni contamination. These results show the bioaccumulation patterns of TEs in C. nodosa, and can be used to design biomonitoring programs.
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Affiliation(s)
- Loubna Boutahar
- BioBio Research Center, BioEcoGen Laboratory, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, B.P. 1014 RP, 10106 Rabat, Morocco; Laboratorio de Biología Marina, Departamento de Zoologia, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain.
| | - Free Espinosa
- Laboratorio de Biología Marina, Departamento de Zoologia, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain
| | - Juan Sempere-Valverde
- Laboratorio de Biología Marina, Departamento de Zoologia, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain
| | - Mohamed Selfati
- National Institute of Fisheries Research (INRH), 13Bd Zerktouni, BP 493, Nador, Morocco
| | - Hocein Bazairi
- BioBio Research Center, BioEcoGen Laboratory, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, B.P. 1014 RP, 10106 Rabat, Morocco; Institute of Life and Earth Sciences, University of Gibraltar, Europa Point Campus, GX11 1AA, Gibraltar
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4
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Mishra AK, Cabaço S, de Los Santos CB, Apostolaki ET, Vizzini S, Santos R. Long-term effects of elevated CO 2 on the population dynamics of the seagrass Cymodocea nodosa: Evidence from volcanic seeps. MARINE POLLUTION BULLETIN 2021; 162:111824. [PMID: 33162054 DOI: 10.1016/j.marpolbul.2020.111824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/25/2020] [Accepted: 10/30/2020] [Indexed: 06/11/2023]
Abstract
Population reconstruction techniques was used to assess for the first time the population dynamics of a seagrass, Cymodocea nodosa, exposed to long-term elevated CO2 near three volcanic seeps and compared them with reference sites away from the seeps. Under high CO2, the density of shoots and of individuals (apical shoots), and the vertical and horizontal elongation and production rates, were higher than at the reference sites. Nitrogen limitation effects on rhizome elongation and production rates and on biomass were more evident than CO2 as these were highest at the location where the limitation of nitrogen was highest. At the seep where the availability of CO2 was highest and nitrogen lowest, density of shoots and individuals were highest, probably due to CO2 effects on shoot differentiation and induced reproductive output, respectively. At the three seeps, there was higher short- and long-term shoot recruitment than at the reference sites, and growth rates was around zero, indicating that elevated CO2 increases the turnover of C. nodosa shoots.
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Affiliation(s)
- A K Mishra
- Marine Plant Ecology Research Group (ALGAE), Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal; School of Biological and Marine Sciences, Faculty of Science and Engineering, University of Plymouth, Portland Square, Drake Circus, Plymouth PL48LA, UK.
| | - S Cabaço
- Marine Plant Ecology Research Group (ALGAE), Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal
| | - C B de Los Santos
- Marine Plant Ecology Research Group (ALGAE), Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal
| | - E T Apostolaki
- Institute of Oceanography, Hellenic Center for Marine Research (HCMR), PO Box 2214, 71003 Heraklion-Crete, Greece
| | - S Vizzini
- Department of Earth and Marine Sciences, University of Palermo, via Archirafi 18, 90123 Palermo, Italy; CoNISMa, Piazzale Flaminio 9, 00196 Roma, Italy
| | - R Santos
- Marine Plant Ecology Research Group (ALGAE), Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal
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Leaf proteome modulation and cytological features of seagrass Cymodocea nodosa in response to long-term high CO 2 exposure in volcanic vents. Sci Rep 2020; 10:22332. [PMID: 33339849 PMCID: PMC7749125 DOI: 10.1038/s41598-020-78764-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 11/24/2020] [Indexed: 11/22/2022] Open
Abstract
Seagrass Cymodocea nodosa was sampled off the Vulcano island, in the vicinity of a submarine volcanic vent. Leaf samples were collected from plants growing in a naturally acidified site, influenced by the long-term exposure to high CO2 emissions, and compared with others collected in a nearby meadow living at normal pCO2 conditions. The differential accumulated proteins in leaves growing in the two contrasting pCO2 environments was investigated. Acidified leaf tissues had less total protein content and the semi-quantitative proteomic comparison revealed a strong general depletion of proteins belonging to the carbon metabolism and protein metabolism. A very large accumulation of proteins related to the cell respiration and to light harvesting process was found in acidified leaves in comparison with those growing in the normal pCO2 site. The metabolic pathways linked to cytoskeleton turnover also seemed affected by the acidified condition, since a strong reduction in the concentration of cytoskeleton structural proteins was found in comparison with the normal pCO2 leaves. Results coming from the comparative proteomics were validated by the histological and cytological measurements, suggesting that the long lasting exposure and acclimation of C. nodosa to the vents involved phenotypic adjustments that can offer physiological and structural tools to survive the suboptimal conditions at the vents vicinity.
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m 6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms. Int J Mol Sci 2020; 21:ijms21207508. [PMID: 33053767 PMCID: PMC7589960 DOI: 10.3390/ijms21207508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 01/08/2023] Open
Abstract
Circadian regulations are essential for enabling organisms to synchronize physiology with environmental light-dark cycles. Post-transcriptional RNA modifications still represent an understudied level of gene expression regulation in plants, although they could play crucial roles in environmental adaptation. N6-methyl-adenosine (m6A) is the most prevalent mRNA modification, established by "writer" and "eraser" proteins. It influences the clockwork in several taxa, but only few studies have been conducted in plants and none in marine plants. Here, we provided a first inventory of m6A-related genes in seagrasses and investigated daily changes in the global RNA methylation and transcript levels of writers and erasers in Cymodocea nodosa and Zostera marina. Both species showed methylation peaks during the dark period under the same photoperiod, despite exhibiting asynchronous changes in the m6A profile and related gene expression during a 24-h cycle. At contrasting latitudes, Z. marina populations displayed overlapping daily patterns of the m6A level and related gene expression. The observed rhythms are characteristic for each species and similar in populations of the same species with different photoperiods, suggesting the existence of an endogenous circadian control. Globally, our results indicate that m6A RNA methylation could widely contribute to circadian regulation in seagrasses, potentially affecting the photo-biological behaviour of these plants.
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Riccio G, Ruocco N, Mutalipassi M, Costantini M, Zupo V, Coppola D, de Pascale D, Lauritano C. Ten-Year Research Update Review: Antiviral Activities from Marine Organisms. Biomolecules 2020; 10:biom10071007. [PMID: 32645994 PMCID: PMC7407529 DOI: 10.3390/biom10071007] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/25/2020] [Accepted: 06/28/2020] [Indexed: 02/08/2023] Open
Abstract
Oceans cover more than 70 percent of the surface of our planet and are characterized by huge taxonomic and chemical diversity of marine organisms. Several studies have shown that marine organisms produce a variety of compounds, derived from primary or secondary metabolism, which may have antiviral activities. In particular, certain marine metabolites are active towards a plethora of viruses. Multiple mechanisms of action have been found, as well as different targets. This review gives an overview of the marine-derived compounds discovered in the last 10 years. Even if marine organisms produce a wide variety of different compounds, there is only one compound available on the market, Ara-A, and only another one is in phase I clinical trials, named Griffithsin. The recent pandemic emergency caused by SARS-CoV-2, also known as COVID-19, highlights the need to further invest in this field, in order to shed light on marine compound potentiality and discover new drugs from the sea.
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Affiliation(s)
- Gennaro Riccio
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Nadia Ruocco
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Mirko Mutalipassi
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Maria Costantini
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Valerio Zupo
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
| | - Daniela Coppola
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
- Institute of Biosciences and BioResources (IBBR), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Donatella de Pascale
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Chiara Lauritano
- Marine Biotechnology Department, Stazione Zoologica Anton Dohrn, CAP, 80121 Naples, Italy; (G.R.); (N.R.); (M.M.); (M.C.); (V.Z.); (D.C.); (D.d.P.)
- Correspondence: ; Tel.: +39-081-5833-221
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8
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Mishra AK, Santos R, Hall-Spencer JM. Elevated trace elements in sediments and seagrasses at CO 2 seeps. MARINE ENVIRONMENTAL RESEARCH 2020; 153:104810. [PMID: 31733909 DOI: 10.1016/j.marenvres.2019.104810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 09/29/2019] [Accepted: 10/04/2019] [Indexed: 06/10/2023]
Abstract
Seagrasses often occur around shallow marine CO2 seeps, allowing assessment of trace metal accumulation. Here, we measured Cd, Cu, Hg, Ni, Pb and Zn levels at six CO2 seeps and six reference sites in the Mediterranean. Some seep sediments had elevated metal concentrations; an extreme example was Cd which was 43x more concentrated at a seep site than its corresponding reference site. Three seeps had metal levels that were predicted to adversely affect marine biota, namely Vulcano (for Hg), Ischia (for Cu) and Paleochori (for Cd and Ni). There were higher-than-sediment levels of Zn and Ni in Posidonia oceanica and of Zn in Cymodocea nodosa, particularly in roots. High levels of Cu were found in Ischia seep sediments, yet seagrass was abundant there, and the plants contained low levels of Cu. Differences in bioavailability and toxicity of trace elements helps explain why seagrasses can be abundant at some CO2 seeps but not at others.
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Affiliation(s)
- A K Mishra
- Centre for Marine Sciences, University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal; School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL48A, UK.
| | - R Santos
- Centre for Marine Sciences, University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - J M Hall-Spencer
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL48A, UK; Shimoda Marine Research Centre, University of Tsukuba, Shizuoka, 415-0025, Japan
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9
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González-Delgado S, Hernández JC. The Importance of Natural Acidified Systems in the Study of Ocean Acidification: What Have We Learned? ADVANCES IN MARINE BIOLOGY 2018; 80:57-99. [PMID: 30368306 DOI: 10.1016/bs.amb.2018.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Human activity is generating an excess of atmospheric CO2, resulting in what we know as ocean acidification, which produces changes in marine ecosystems. Until recently, most of the research in this area had been done under small-scale, laboratory conditions, using few variables, few species and few life cycle stages. These limitations raise questions about the reproducibility of the environment and about the importance of indirect effects and synergies in the final results of these experiments. One way to address these experimental problems is by conducting studies in situ, in natural areas where expected future pH conditions already occur, such as CO2 vent systems. In the present work, we compile and discuss the latest research carried out in these natural laboratories, with the objective to summarize their advantages and disadvantages for research to improve these investigations so they can better help us understand how the oceans of the future will change.
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Affiliation(s)
- Sara González-Delgado
- Marine Community Ecology and Climate Change, Departamento de Biología Animal, Edafología y Geología, Facultad de Ciencias (Biología), Universidad de La Laguna, Tenerife, Canary Islands, Spain
| | - José Carlos Hernández
- Marine Community Ecology and Climate Change, Departamento de Biología Animal, Edafología y Geología, Facultad de Ciencias (Biología), Universidad de La Laguna, Tenerife, Canary Islands, Spain.
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10
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Scartazza A, Moscatello S, Gavrichkova O, Buia MC, Lauteri M, Battistelli A, Lorenti M, Garrard SL, Calfapietra C, Brugnoli E. Carbon and nitrogen allocation strategy in Posidonia oceanica is altered by seawater acidification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:954-964. [PMID: 28724227 DOI: 10.1016/j.scitotenv.2017.06.084] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/08/2017] [Accepted: 06/10/2017] [Indexed: 05/05/2023]
Abstract
Rising atmospheric CO2 causes ocean acidification that represents one of the major ecological threats for marine biota. We tested the hypothesis that long-term exposure to increased CO2 level and acidification in a natural CO2 vent system alters carbon (C) and nitrogen (N) metabolism in Posidonia oceanica L. (Delile), affecting its resilience, or capability to restore the physiological homeostasis, and the nutritional quality of organic matter available for grazers. Seawater acidification decreased the C to N ratio in P. oceanica tissues and increased grazing rate, shoot density, leaf proteins and asparagine accumulation in rhizomes, while the maximum photochemical efficiency of photosystem II was unaffected. The 13C-dilution in both structural and non-structural C metabolites in the acidified site indicated quali-quantitative changes of C source and/or increased isotopic fractionation during C uptake and carboxylation associated with the higher CO2 level. The decreased C:N ratio in the acidified site suggests an increased N availability, leading to a greater storage of 15N-enriched compounds in rhizomes. The amount of the more dynamic C storage form, sucrose, decreased in rhizomes of the acidified site in response to the enhanced energy demand due to higher shoot recruitment and N compound synthesis, without affecting starch reserves. The ability to modulate the balance between stable and dynamic C reserves could represent a key ecophysiological mechanism for P. oceanica resilience under environmental perturbation. Finally, alteration in C and N dynamics promoted a positive contribution of this seagrass to the local food web.
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Affiliation(s)
- Andrea Scartazza
- Istituto di Biologia Agroambientale e Forestale, Consiglio Nazionale delle Ricerche, Via Salaria km 29,300, 00016 Monterotondo Scalo, RM, Italy; Istituto di Biologia Agroambientale e Forestale, Consiglio Nazionale delle Ricerche, Via G. Marconi 2, 05010 Porano, TR, Italy.
| | - Stefano Moscatello
- Istituto di Biologia Agroambientale e Forestale, Consiglio Nazionale delle Ricerche, Via G. Marconi 2, 05010 Porano, TR, Italy.
| | - Olga Gavrichkova
- Istituto di Biologia Agroambientale e Forestale, Consiglio Nazionale delle Ricerche, Via G. Marconi 2, 05010 Porano, TR, Italy
| | | | - Marco Lauteri
- Istituto di Biologia Agroambientale e Forestale, Consiglio Nazionale delle Ricerche, Via G. Marconi 2, 05010 Porano, TR, Italy
| | - Alberto Battistelli
- Istituto di Biologia Agroambientale e Forestale, Consiglio Nazionale delle Ricerche, Via G. Marconi 2, 05010 Porano, TR, Italy
| | - Maurizio Lorenti
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | | | - Carlo Calfapietra
- Istituto di Biologia Agroambientale e Forestale, Consiglio Nazionale delle Ricerche, Via G. Marconi 2, 05010 Porano, TR, Italy
| | - Enrico Brugnoli
- Istituto di Biologia Agroambientale e Forestale, Consiglio Nazionale delle Ricerche, Via G. Marconi 2, 05010 Porano, TR, Italy
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11
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Campbell JE, Fourqurean JW. Does Nutrient Availability Regulate Seagrass Response to Elevated CO2? Ecosystems 2017. [DOI: 10.1007/s10021-017-0212-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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12
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Tutar O, Marín-Guirao L, Ruiz JM, Procaccini G. Antioxidant response to heat stress in seagrasses. A gene expression study. MARINE ENVIRONMENTAL RESEARCH 2017; 132:94-102. [PMID: 29126631 DOI: 10.1016/j.marenvres.2017.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/16/2017] [Accepted: 10/22/2017] [Indexed: 05/03/2023]
Abstract
Seawater warming associated to the ongoing climate change threatens functioning and survival of keystone coastal benthic species such as seagrasses. Under elevated temperatures, the production of reactive oxygen species (ROS) is increased and plants must activate their antioxidant defense mechanisms to protect themselves from oxidative damage. Here we explore from a molecular perspective the ability of Mediterranean seagrasses to activate heat stress response mechanisms, with particular focus on antioxidants. The level of expression of targeted genes was analyzed in shallow and deep plants of the species Posidonia oceanica and in shallow plants of Cymodocea nodosa along an acute heat exposure of several days and after recovery. The overall gene expression response of P. oceanica was more intense and complete than in C. nodosa and reflected a higher oxidative stress level during the experimental heat exposure. The strong activation of genes with chaperone activity (heat shock proteins and a luminal binding protein) just in P. oceanica plants, suggested the higher sensitivity of the species to increased temperatures. In spite of the interspecific differences, genes from the superoxide dismutase (SOD) family seem to play a pivotal role in the thermal stress response of Mediterranean seagrasses as previously reported for other marine plant species. Shallow and deep P. oceanica ecotypes showed a different timing of response to heat. Shallow plants early responded to heat and after a few days relaxed their response which suggests a successful early metabolic adjustment. The response of deep plants was delayed and their recovery incomplete evidencing a lower resilience to heat in respect to shallow ecotypes. Moreover, shallow ecotypes showed some degree of pre-adaptation to heat as most analyzed genes showed higher constitutive expression levels than in deep ecotypes. The recurrent exposure of shallow plants to elevated summer temperatures has likely endowed them with a higher basal level of antioxidant defense and a faster responsiveness to warming than deep plants. Our findings match with previous physiological studies and supported the idea that warming will differently impact Mediterranean seagrass meadows depending on the species as well as on the depth (i.e. thermal regimen) at which the meadow grows. The increase in the incidence of summer heat waves could therefore produce a significant change in the distribution and composition of Mediterranean seagrass meadows with considerable consequences for the functioning of the whole ecosystem and for the socio-economic services that these ecosystems offer to the riverine populations.
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Affiliation(s)
- O Tutar
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; Department of Earth and Environmental Sciences, University Milano-Bicocca, Piazza della Scienza, 4-20126 Milano, Italy
| | - L Marín-Guirao
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| | - J M Ruiz
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography, C/ Varadero, 30740 San Pedro del Pinatar, Murcia, Spain
| | - G Procaccini
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
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Ravaglioli C, Lauritano C, Buia MC, Balestri E, Capocchi A, Fontanini D, Pardi G, Tamburello L, Procaccini G, Bulleri F. Nutrient Loading Fosters Seagrass Productivity Under Ocean Acidification. Sci Rep 2017; 7:13732. [PMID: 29062025 PMCID: PMC5653774 DOI: 10.1038/s41598-017-14075-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 09/20/2017] [Indexed: 12/04/2022] Open
Abstract
The effects of climate change are likely to be dependent on local settings. Nonetheless, the compounded effects of global and regional stressors remain poorly understood. Here, we used CO2 vents to assess how the effects of ocean acidification on the seagrass, Posidonia oceanica, and the associated epiphytic community can be modified by enhanced nutrient loading. P. oceanica at ambient and low pH sites was exposed to three nutrient levels for 16 months. The response of P. oceanica to experimental conditions was assessed by combining analyses of gene expression, plant growth, photosynthetic pigments and epiphyte loading. At low pH, nutrient addition fostered plant growth and the synthesis of photosynthetic pigments. Overexpression of nitrogen transporter genes following nutrient additions at low pH suggests enhanced nutrient uptake by the plant. In addition, enhanced nutrient levels reduced the expression of selected antioxidant genes in plants exposed to low pH and increased epiphyte cover at both ambient and low pH. Our results show that the effects of ocean acidification on P. oceanica depend upon local nutrient concentration. More generally, our findings suggest that taking into account local environmental settings will be crucial to advance our understanding of the effects of global stressors on marine systems.
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Affiliation(s)
- Chiara Ravaglioli
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna, 1, 56126 Pisa, Italy.
| | - Chiara Lauritano
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | | | - Elena Balestri
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna, 1, 56126 Pisa, Italy
| | - Antonella Capocchi
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna, 1, 56126 Pisa, Italy
| | - Debora Fontanini
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna, 1, 56126 Pisa, Italy
| | - Giuseppina Pardi
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna, 1, 56126 Pisa, Italy
| | - Laura Tamburello
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna, 1, 56126 Pisa, Italy.,CoNISMa, Piazzale Flaminio, 9, 00196, Roma, Italy
| | | | - Fabio Bulleri
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna, 1, 56126 Pisa, Italy
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14
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Jiang Z, Kumar M, Padula MP, Pernice M, Kahlke T, Kim M, Ralph PJ. Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis. FRONTIERS IN PLANT SCIENCE 2017; 8:1416. [PMID: 28861098 PMCID: PMC5559503 DOI: 10.3389/fpls.2017.01416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/31/2017] [Indexed: 05/31/2023]
Abstract
The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis. All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis. However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2% PVPP and protease inhibitors. Further, the extracted proteins were solubilized in 0.5% of zwitterionic detergent (C7BzO) instead of 4% CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoenolpyruvate carboxylase (PEPC-a key enzyme for carbon metabolism). This optimized protein extraction method will be a significant stride toward seagrass proteome mining and identifying the protein biomarkers to stress response of seagrasses under the scenario of global climate change and anthropogenic perturbations.
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Affiliation(s)
- Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of SciencesGuangzhou, China
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Manoj Kumar
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Matthew P. Padula
- Proteomics Core Facility, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Mathieu Pernice
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Tim Kahlke
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Mikael Kim
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
| | - Peter J. Ralph
- Climate Change Cluster (C3), Faculty of Science, University of Technology Sydney (UTS)Sydney, NSW, Australia
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15
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Ruocco M, Musacchia F, Olivé I, Costa MM, Barrote I, Santos R, Sanges R, Procaccini G, Silva J. Genomewide transcriptional reprogramming in the seagrass Cymodocea nodosa under experimental ocean acidification. Mol Ecol 2017; 26:4241-4259. [PMID: 28614601 DOI: 10.1111/mec.14204] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/18/2017] [Accepted: 05/30/2017] [Indexed: 12/29/2022]
Abstract
Here, we report the first use of massive-scale RNA-sequencing to explore seagrass response to CO2 -driven ocean acidification (OA). Large-scale gene expression changes in the seagrass Cymodocea nodosa occurred at CO2 levels projected by the end of the century. C. nodosa transcriptome was obtained using Illumina RNA-Seq technology and de novo assembly, and differential gene expression was explored in plants exposed to short-term high CO2 /low pH conditions. At high pCO2 , there was a significant increased expression of transcripts associated with photosynthesis, including light reaction functions and CO2 fixation, and also to respiratory pathways, specifically for enzymes involved in glycolysis, in the tricarboxylic acid cycle and in the energy metabolism of the mitochondrial electron transport. The upregulation of respiratory metabolism is probably supported by the increased availability of photosynthates and increased energy demand for biosynthesis and stress-related processes under elevated CO2 and low pH. The upregulation of several chaperones resembling heat stress-induced changes in gene expression highlighted the positive role these proteins play in tolerance to intracellular acid stress in seagrasses. OA further modifies C. nodosa secondary metabolism inducing the transcription of enzymes related to biosynthesis of carbon-based secondary compounds, in particular the synthesis of polyphenols and isoprenoid compounds that have a variety of biological functions including plant defence. By demonstrating which physiological processes are most sensitive to OA, this research provides a major advance in the understanding of seagrass metabolism in the context of altered seawater chemistry from global climate change.
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Affiliation(s)
- Miriam Ruocco
- CCMar-Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | - Irene Olivé
- CCMar-Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Monya M Costa
- CCMar-Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Isabel Barrote
- CCMar-Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Rui Santos
- CCMar-Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | | | - João Silva
- CCMar-Centre of Marine Sciences, University of Algarve, Faro, Portugal
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16
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Rasmusson LM, Lauritano C, Procaccini G, Gullström M, Buapet P, Björk M. Respiratory oxygen consumption in the seagrass Zostera marina varies on a diel basis and is partly affected by light. MARINE BIOLOGY 2017; 164:140. [PMID: 28596620 PMCID: PMC5446554 DOI: 10.1007/s00227-017-3168-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/17/2017] [Indexed: 06/07/2023]
Abstract
The seagrass Zostera marina is an important marine ecosystem engineer, greatly influencing oxygen and carbon fluctuations in temperate coastal areas. Although photosynthetically driven gas fluxes are well studied, the impact of the plant's mitochondrial respiration on overall CO2 and O2 fluxes in marine vegetated areas is not yet understood. Likewise, the gene expression in relation to the respiratory pathway has not been well analyzed in seagrasses. This study uses a combined approach, studying respiratory oxygen consumption rates in darkness simultaneously with changes in gene expression, with the aim of examining how respiratory oxygen consumption fluctuates on a diel basis. Measurements were first made in a field study where samples were taken directly from the ocean to the laboratory for estimations of respiratory rates. This was followed by a laboratory study where measurements of respiration and expression of genes known to be involved in mitochondrial respiration were conducted for 5 days under light conditions mimicking natural summer light (i.e., 15 h of light and 9 h of darkness), followed by 3 days of constant darkness to detect the presence of a potential circadian clock. In the field study, there was a clear diel variation in respiratory oxygen consumption with the highest rates in the late evening and at night (0.766 and 0.869 µmol O2 m-2 s-1, respectively). These repetitive diel patterns were not seen in the laboratory, where water conditions (temperature, pH, and oxygen) showed minor fluctuations and only light varied. The gene expression analysis did not give clear evidence on drivers behind the respiratory fluxes; however, expression levels of the selected genes generally increased when the seagrass was kept in constant darkness. While light may influence mitochondrial respiratory fluxes, it appears that other environmental factors (e.g., temperature, pH, or oxygen) could be of significance too. As seagrasses substantially alter the proportions of both oxygen and inorganic carbon in the water column and respiration is a great driver of these alterations, we propose that acknowledging the presence of respiratory fluctuations in nature should be considered when estimating coastal carbon budgets. As dark respiration in field at midnight was approximately doubled from that of midday, great over-, or underestimations of the respiratory carbon dioxide release from seagrasses could be made if values are just obtained at one specific time point and considered constant.
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Affiliation(s)
- Lina M. Rasmusson
- Seagrass Ecology and Physiology Research Group, Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Chiara Lauritano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Martin Gullström
- Seagrass Ecology and Physiology Research Group, Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Pimchanok Buapet
- Seagrass Ecology and Physiology Research Group, Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
- Department of Biology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112 Thailand
| | - Mats Björk
- Seagrass Ecology and Physiology Research Group, Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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