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Qi W, Jiang Z, Long X, Liu Y, Fang Y, Egodauyana UT, Chen X, Liu S, Wu Y, Huang X. The metabolic network response and tolerance mechanism of Thalassia hemprichii under high sulfide based on widely targeted metabolome and transcriptome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175702. [PMID: 39179040 DOI: 10.1016/j.scitotenv.2024.175702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Costal eutrophication leads to increased sulfide levels in sediments, which has been identified as a major cause of the global decline in seagrass beds. The seagrass Thalassia hemprichii, a dominant tropical species in the Indo-Pacific, is facing a potential threat from sulfide, which can be easily reduced from sulfate in porewater under the influence of global climate change and eutrophication. However, its metabolic response and tolerance mechanisms to high sulfide remain unclear. Thus, the current study investigated the physiological responses and programmed metabolic networks of T. hemprichii through a three-week mesocosm experiment, integrating physiology, stable isotope, widely targeted metabolomics, transcriptomics, and microbial diversity assessments. High sulfide reduced the sediment microbial diversity, while increased sediment sulfate reduced bacterial abundance and δ34S. The exposure to sulfide enhanced root δ34S while decreased leaf δ34S in T. hemprichii. High sulfide was shown to inhibit photosynthesis via damaging PSII, which further reduced ATP production. In response, abundant up-regulated differentially expressed genes in energy metabolism, especially in oxidative phosphorylation, were activated to compensate high energy requirement. High sulfide also promoted autophagy by overexpressing the genes related to phagocytosis and phagolysosome. Meanwhile, metabolomic profiling revealed that the contents of many primary metabolites, such as carbohydrates and amino acids, were reduced in both leaves and roots, likely to provide more energy and synthesize stress-responsive secondary metabolites. Genes related to nitrate reduction and transportation were up-regulated to promote N uptake for sulfide detoxification. High sulfide levels specifically enhanced thiamine in roots, while increased jasmonic acid and flavonoid levels in leaves. The distinct differences in metabolism between roots and leaves might be related to sulfide levels and the growth-defense trade-off. Collectively, our work highlights the specific mechanisms underlying the response and tolerance of T. hemprichii to high sulfide, providing new insights into seagrass strategies for resisting sulfide.
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Affiliation(s)
- Wenqian Qi
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China.
| | - Xu Long
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yijun Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Uditha Thejan Egodauyana
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xian Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China; Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China.
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Rede JE, Breitbart M, Lundquist C, Nagasaki K, Hewson I. Diverse RNA viruses discovered in multiple seagrass species. PLoS One 2024; 19:e0302314. [PMID: 39196976 PMCID: PMC11356395 DOI: 10.1371/journal.pone.0302314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 04/01/2024] [Indexed: 08/30/2024] Open
Abstract
Seagrasses are marine angiosperms that form highly productive and diverse ecosystems. These ecosystems, however, are declining worldwide. Plant-associated microbes affect critical functions like nutrient uptake and pathogen resistance, which has led to an interest in the seagrass microbiome. However, despite their significant role in plant ecology, viruses have only recently garnered attention in seagrass species. In this study, we produced original data and mined publicly available transcriptomes to advance our understanding of RNA viral diversity in Zostera marina, Zostera muelleri, Zostera japonica, and Cymodocea nodosa. In Z. marina, we present evidence for additional Zostera marina amalgavirus 1 and 2 genotypes, and a complete genome for an alphaendornavirus previously evidenced by an RNA-dependent RNA polymerase gene fragment. In Z. muelleri, we present evidence for a second complete alphaendornavirus and near complete furovirus. Both are novel, and, to the best of our knowledge, this marks the first report of a furovirus infection naturally occurring outside of cereal grasses. In Z. japonica, we discovered genome fragments that belong to a novel strain of cucumber mosaic virus, a prolific pathogen that depends largely on aphid vectoring for host-to-host transmission. Lastly, in C. nodosa, we discovered two contigs that belong to a novel virus in the family Betaflexiviridae. These findings expand our knowledge of viral diversity in seagrasses and provide insight into seagrass viral ecology.
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Affiliation(s)
- Jordan E. Rede
- Department of Microbiology, Cornell University, Ithaca, NY, United States of America
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL, United States of America
| | - Carolyn Lundquist
- National Institute of Water and Atmospheric Research, Hamilton, New Zealand
- School of Environment, The University of Auckland, Auckland, New Zealand
| | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, Nankoku, Kochi, Japan
| | - Ian Hewson
- Department of Microbiology, Cornell University, Ithaca, NY, United States of America
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Nguyen HM, Hong UVT, Ruocco M, Dattolo E, Marín-Guirao L, Pernice M, Procaccini G. Thermo-priming triggers species-specific physiological and transcriptome responses in Mediterranean seagrasses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108614. [PMID: 38626655 DOI: 10.1016/j.plaphy.2024.108614] [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: 12/10/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/18/2024]
Abstract
Heat-priming improves plants' tolerance to a recurring heat stress event. The underlying molecular mechanisms of heat-priming are largely unknown in seagrasses. Here, ad hoc mesocosm experiments were conducted with two Mediterranean seagrass species, Posidonia oceanica and Cymodocea nodosa. Plants were first exposed to heat-priming, followed by a heat-triggering event. A comprehensive assessment of plant stress response across different levels of biological organization was performed at the end of the triggering event. Morphological and physiological results showed an improved response of heat-primed P. oceanica plants while in C. nodosa both heat- and non-primed plants enhanced their growth rates at the end of the triggering event. As resulting from whole transcriptome sequencing, molecular functions related to several cellular compartments and processes were involved in the response to warming of non-primed plants, while the response of heat-primed plants involved a limited group of processes. Our results suggest that seagrasses acquire a primed state during the priming event, that eventually gives plants the ability to induce a more energy-effective response when the thermal stress event recurs. Different species may differ in their ability to perform an improved heat stress response after priming. This study provides pioneer molecular insights into the emerging topic of seagrass stress priming and may benefit future studies in the field.
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Affiliation(s)
- Hung Manh Nguyen
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Uyen V T Hong
- La Trobe University, AgriBio Building, Bundoora, 3086, VIC, Australia; Department of Plant Biotechnology & Biotransformation, University of Science, Vietnam National University, 700000, Ho Chi Minh City, Viet Nam
| | - Miriam Ruocco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Emanuela Dattolo
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy
| | - Lázaro Marín-Guirao
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; Oceanographic Center of Murcia, Seagrass Ecology Group, Spanish Institute of Oceanography (IEO-CSIC), C/Varadero, San Pedro del Pinatar, 30740, Murcia, Spain.
| | - Mathieu Pernice
- Faculty of Science, Climate Change Cluster (C3), University of Technology Sydney, Sydney, 2007, NSW, Australia
| | - Gabriele Procaccini
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133, Palermo, Italy
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Rodríguez-Rojas F, Navarrete C, Rámila C, Tapia-Reyes P, Celis-Plá PSM, González C, Pereira-Rojas J, Blanco-Murillo F, Moreno P, Gutiérrez-Campos C, Sánchez-Lizaso JL, Sáez CA. Transcriptomic profiles and diagnostic biomarkers in the Mediterranean seagrasses Posidonia oceanica and Cymodocea nodosa reveal mechanistic insights of adaptative strategies upon desalination brine stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170326. [PMID: 38266720 DOI: 10.1016/j.scitotenv.2024.170326] [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: 09/17/2023] [Revised: 12/26/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Seawater desalination by reverse osmosis is growing exponentially due to water scarcity. Byproducts of this process (e.g. brines), are generally discharged directly into the coastal ecosystem, causing detrimental effects, on benthic organisms. Understanding the cellular stress response of these organisms (biomarkers), could be crucial for establishing appropriate salinity thresholds for discharged brines. Early stress biomarkers can serve as valuable tools for monitoring the health status of brine-impacted organisms, enabling the prediction of long-term irreversible damage caused by the desalination industry. In this study, we conducted laboratory-controlled experiments to assess cellular and molecular biomarkers against brine exposure in two salinity-sensitive Mediterranean seagrasses: Posidonia oceanica and Cymodocea nodosa. Treatments involved exposure to 39, 41, and 43 psu, for 6 h and 7 days. Results indicated that photosynthetic performance remained unaffected across all treatments. However, under 43 psu, P. oceanica and C. nodosa exhibited lipid oxidative damage, which occurred earlier in P. oceanica. Additionally, P. oceanica displayed an antioxidant response at higher salinities by accumulating phenolic compounds within 6 h and ascorbate within 7 d; whereas for C. nodosa the predominant antioxidant mechanisms were phenolic compounds accumulation and total radical scavenging activity, which was evident after 7 d of brines exposure. Finally, transcriptomic analyses in P. oceanica exposed to 43 psu for 7 days revealed a poor up-regulation of genes associated with brassinosteroid response and abiotic stress response, while a high down-regulation of genes related to primary metabolism was detected. In C. nodosa, up-regulated genes were involved in DNA repair, cell cycle regulation, and reproduction, while down-regulated genes were mainly associated with photosynthesis and ribosome assembly. Overall, these findings suggest that 43 psu is a critical salinity-damage threshold for both seagrasses; and despite the moderate overexpression of several transcripts that could confer salt tolerance, genes involved in essential biological processes were severely downregulated.
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Affiliation(s)
- Fernanda Rodríguez-Rojas
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile; Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Subida Leopoldo Carvallo 270, 2360004, Valparaíso, Chile. Valparaíso, Chile
| | - Camilo Navarrete
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile; Doctorado Interdisciplinario en Ciencias Ambientales, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Subida Leopoldo Carvallo 270, 2360004, Valparaíso, Chile
| | - Consuelo Rámila
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile
| | - Patricio Tapia-Reyes
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Santo Tomás. Av. Ejército 146, 8370003, Santiago, Chile
| | - Paula S M Celis-Plá
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile; Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Subida Leopoldo Carvallo 270, 2360004, Valparaíso, Chile. Valparaíso, Chile
| | - Christian González
- Escuela de Obras Civiles, Universidad Diego Portales. Av. Ejército 441, 8370191, Santiago, Chile
| | - Jeniffer Pereira-Rojas
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile; Doctorado Interdisciplinario en Ciencias Ambientales, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Subida Leopoldo Carvallo 270, 2360004, Valparaíso, Chile
| | - Fabio Blanco-Murillo
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile; Doctorado Interdisciplinario en Ciencias Ambientales, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Subida Leopoldo Carvallo 270, 2360004, Valparaíso, Chile; Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, Alicante, Spain
| | - Pablo Moreno
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile
| | - Catalina Gutiérrez-Campos
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile
| | - José Luis Sánchez-Lizaso
- Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, Alicante, Spain; Ciencias del Mar Universidad de Alicante, Unidad Asociada al CSIC por el IEO, Carretera de San Vicente del Raspeig s/n, 03690, Alicante, Spain
| | - Claudio A Sáez
- Laboratorio de Investigación Ambiental Acuático, HUB AMBIENTAL UPLA, Universidad de Playa Ancha. Subida Leopoldo Carvallo 207, acceso Hospital del Salvador, 2360004, Valparaíso, Chile; Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha. Subida Leopoldo Carvallo 270, 2360004, Valparaíso, Chile. Valparaíso, Chile; Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, Alicante, Spain.
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Ravaglioli C, De Marchi L, Anselmi S, Dattolo E, Fontanini D, Pretti C, Procaccini G, Rilov G, Renzi M, Silverman J, Bulleri F. Ocean acidification impairs seagrass performance under thermal stress in shallow and deep water. ENVIRONMENTAL RESEARCH 2024; 241:117629. [PMID: 37967703 DOI: 10.1016/j.envres.2023.117629] [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: 08/09/2023] [Revised: 10/21/2023] [Accepted: 11/07/2023] [Indexed: 11/17/2023]
Abstract
Despite the effects of ocean acidification (OA) on seagrasses have been widely investigated, predictions of seagrass performance under future climates need to consider multiple environmental factors. Here, we performed a mesocosm study to assess the effects of OA on shallow and deep Posidonia oceanica plants. The experiment was run in 2021 and repeated in 2022, a year characterized by a prolonged warm water event, to test how the effects of OA on plants are modulated by thermal stress. The response of P. oceanica to experimental conditions was investigated at different levels of biological organization. Under average seawater temperature, there were no effects of OA in both shallow and deep plants, indicating that P. oceanica is not limited by current inorganic carbon concentration, regardless of light availability. In contrast, under thermal stress, exposure of plants to OA increased lipid peroxidation and decreased photosynthetic performance, with deep plants displaying higher levels of heat stress, as indicated by the over-expression of stress-related genes and the activation of antioxidant systems. In addition, warming reduced plant growth, regardless of seawater CO2 and light levels, suggesting that thermal stress may play a fundamental role in the future development of seagrass meadows. Our results suggest that OA may exacerbate the negative effects of future warming on seagrasses.
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Affiliation(s)
- Chiara Ravaglioli
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy.
| | - Lucia De Marchi
- Dipartimento di Scienze Veterinarie, Università of Pisa, Via Livornese (lato monte), 56122, San Piero a Grado, Pisa, Italy.
| | - Serena Anselmi
- Bioscience Research Center, Via Aurelia Vecchia, 32, 58015, Orbetello, GR, Italy.
| | - Emanuela Dattolo
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; National Biodiversity Future Centre (NBFC), Palermo, Italy.
| | - Debora Fontanini
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy.
| | - Carlo Pretti
- Dipartimento di Scienze Veterinarie, Università of Pisa, Via Livornese (lato monte), 56122, San Piero a Grado, Pisa, Italy; Interuniversity Consortium of Marine Biology and Applied Ecology "G. Bacci" (CIBM), Viale N.Sauro 4, 57128, Livorno, Italy.
| | - Gabriele Procaccini
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy; National Biodiversity Future Centre (NBFC), Palermo, Italy.
| | - Gil Rilov
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel.
| | - Monia Renzi
- Dipartimento di Scienze Della Vita, Università di Trieste, Via Giorgieri, 10, 34127, Trieste, Italy.
| | - Jacob Silverman
- National Institute of Oceanography, Israel Oceanographic and Limnological Research, Haifa, Israel.
| | - Fabio Bulleri
- Dipartimento di Biologia, Università di Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy; Centro Interdipartimentale di Ricerca per Lo Studio Degli Effetti Del Cambiamento Climatico (CIRSEC), Università di Pisa, Italy.
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Single-molecule real-time sequencing of the full-length transcriptome of Halophila beccarii. Sci Rep 2022; 12:16444. [PMID: 36180578 PMCID: PMC9525579 DOI: 10.1038/s41598-022-20988-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/21/2022] [Indexed: 11/24/2022] Open
Abstract
Ecologically, Halophila beccarii Asch. is considered as a colonizing or a pioneer seagrass species and a “tiny but mighty” seagrass species, since it may recover quickly from disturbance generally. The use of transcriptome technology can provide a better understanding of the physiological processes of seagrasses. To date, little is known about the genome and transcriptome information of H. beccarii. In this study, we used single molecule real-time (SMRT) sequencing to obtain full-length transcriptome data and characterize the transcriptome structure. A total of 11,773 of the 15,348 transcripts were successfully annotated in seven databases. In addition, 1573 long non-coding RNAs, 8402 simple sequence repeats and 2567 transcription factors were predicted in all the transcripts. A GO analysis showed that 5843 transcripts were divided into three categories, including biological process (BP), cellular component (CC) and molecular function (MF). In these three categories, metabolic process (1603 transcripts), protein-containing complex (515 transcripts) and binding (3233 transcripts) were the primary terms in BP, CC, and MF, respectively. The major types of transcription factors were involved in MYB-related and NF-YB families. To the best of our knowledge, this is the first report of the transcriptome of H. beccarii using SMRT sequencing technology.
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Ruocco M, Jahnke M, Silva J, Procaccini G, Dattolo E. 2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation. Front Genet 2022; 13:866758. [PMID: 35651946 PMCID: PMC9149362 DOI: 10.3389/fgene.2022.866758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.
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Affiliation(s)
| | - Marlene Jahnke
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - João Silva
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
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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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Entrambasaguas L, Ruocco M, Verhoeven KJF, Procaccini G, Marín-Guirao L. Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress. Sci Rep 2021; 11:14343. [PMID: 34253765 PMCID: PMC8275578 DOI: 10.1038/s41598-021-93606-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
The role of DNA methylation and its interaction with gene expression and transcriptome plasticity is poorly understood, and current insight comes mainly from studies in very few model plant species. Here, we study gene body DNA methylation (gbM) and gene expression patterns in ecotypes from contrasting thermal environments of two marine plants with contrasting life history strategies in order to explore the potential role epigenetic mechanisms could play in gene plasticity and responsiveness to heat stress. In silico transcriptome analysis of CpGO/E ratios suggested that the bulk of Posidonia oceanica and Cymodocea nodosa genes possess high levels of intragenic methylation. We also observed a correlation between gbM and gene expression flexibility: genes with low DNA methylation tend to show flexible gene expression and plasticity under changing conditions. Furthermore, the empirical determination of global DNA methylation (5-mC) showed patterns of intra and inter-specific divergence that suggests a link between methylation level and the plants' latitude of origin and life history. Although we cannot discern whether gbM regulates gene expression or vice versa, or if other molecular mechanisms play a role in facilitating transcriptome responsiveness, our findings point to the existence of a relationship between gene responsiveness and gbM patterns in marine plants.
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Affiliation(s)
- Laura Entrambasaguas
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Miriam Ruocco
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Koen J F Verhoeven
- Terrestrial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Gabriele Procaccini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Lazaro Marín-Guirao
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography, C/Varadero, 30740, San Pedro del Pinatar, Spain
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10
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Zhang Y, Gu Z, Ren Y, Wang L, Zhang J, Liang C, Tong S, Wang Y, Xu D, Zhang X, Ye N. Integrating Transcriptomics and Metabolomics to Characterize Metabolic Regulation to Elevated CO 2 in Chlamydomonas Reinhardtii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:255-275. [PMID: 33689052 DOI: 10.1007/s10126-021-10021-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/14/2021] [Indexed: 05/27/2023]
Abstract
With atmospheric CO2 increasing, a large amount of CO2 is absorbed by oceans and lakes, which changes the carbonate system and affects the survival of aquatic plants, especially microalgae. The main aim of our study was to explore the responses of Chlamydomonas reinhardtii (Chlorophyceae) to elevated CO2 by combined transcriptome and metabolome analysis under three different scenarios: control (CK, 400 ppm), short-term elevated CO2 (ST, 1000 ppm), and long-term elevated CO2 (LT, 1000 ppm). The transcriptomic data showed moderate changes between ST and CK. However, metabolic analysis indicated that fatty acids (FAs) and partial amino acids (AAs) were increased under ST. There was a global downregulation of genes involved in photosynthesis, glycolysis, lipid metabolism, and nitrogen metabolism but increase in the TCA cycle and β-oxidation under LT. Integrated transcriptome and metabolome analyses demonstrated that the nutritional constituents (FAs, AAs) under LT were poor compared with CK, and most genes and metabolites involved in C and N metabolism were significantly downregulated. However, the growth and photosynthesis of cells under LT increased significantly. Thus, C. reinhardtii could form a specific adaptive evolution to elevated CO2, affecting future biogeochemical cycles.
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Affiliation(s)
- Yufei Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, 266042, China
| | - Zipeng Gu
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, 266042, China
| | - Yudong Ren
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, 266042, China
| | - Lu Wang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, 266042, China
| | - Jian Zhang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, 266042, China
| | - Chengwei Liang
- College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, 53 Zhengzhou Road, Qingdao, 266042, China.
| | - Shanying Tong
- School of Life Sciences, Ludong University, 186 Hongqi Middle Road, Yantai, 264025, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China
- National Oceanographic Center, Qingdao, 266071, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China
- National Oceanographic Center, Qingdao, 266071, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China
- National Oceanographic Center, Qingdao, 266071, China
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao, 266071, China.
- National Oceanographic Center, Qingdao, 266071, China.
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11
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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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12
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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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13
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Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L. Life (Basel) 2020; 10:life10030030. [PMID: 32213979 PMCID: PMC7151569 DOI: 10.3390/life10030030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/14/2020] [Accepted: 03/21/2020] [Indexed: 12/29/2022] Open
Abstract
Seagrasses as Posidonia oceanica reproduce mostly by vegetative propagation, which can reduce genetic variability within populations. Since, in clonally propagated species, insurgence of genetic variability can be determined by the activity of transposable elements, we have estimated the activity of such repeat elements by measuring their expression level in the leaves of plants from a Mediterranean site, for which Illumina complementary DNA (cDNA) sequence reads (produced from RNAs isolated by leaves of plants from deep and shallow meadows) were publicly available. Firstly, we produced a collection of retrotransposon-related sequences and then mapped Illumina cDNA reads onto these sequences. With this approach, it was evident that Posidonia retrotransposons are, in general, barely expressed; only nine elements resulted transcribed at levels comparable with those of reference genes encoding tubulins and actins. Differences in transcript abundance were observed according to the superfamily and the lineage to which the retrotransposons belonged. Only small differences were observed between retrotransposon expression levels in leaves of shallow and deep Posidonia meadow stands, whereas one TAR/Tork element resulted differentially expressed in deep plants exposed to heat. It can be concluded that, in P. oceanica, the contribution of retrotransposon activity to genetic variability is reduced, although the nine specific active elements could actually produce new structural variations.
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14
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Zayas-Santiago CC, Rivas-Ubach A, Kuo LJ, Ward ND, Zimmerman RC. Metabolic Profiling Reveals Biochemical Pathways Responsible for Eelgrass Response to Elevated CO 2 and Temperature. Sci Rep 2020; 10:4693. [PMID: 32170204 PMCID: PMC7070064 DOI: 10.1038/s41598-020-61684-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 02/25/2020] [Indexed: 11/17/2022] Open
Abstract
As CO2 levels in Earth’s atmosphere and oceans steadily rise, varying organismal responses may produce ecological losers and winners. Increased ocean CO2 can enhance seagrass productivity and thermal tolerance, providing some compensation for climate warming. However, the metabolic shifts driving the positive response to elevated CO2 by these important ecosystem engineers remain unknown. We analyzed whole-plant performance and metabolic profiles of two geographically distinct eelgrass (Zostera marina L.) populations in response to CO2 enrichment. In addition to enhancing overall plant size, growth and survival, CO2 enrichment increased the abundance of Calvin Cycle and nitrogen assimilation metabolites while suppressing the abundance of stress-related metabolites. Overall metabolome differences between populations suggest that some eelgrass phenotypes may be better suited than others to cope with an increasingly hot and sour sea. Our results suggest that seagrass populations will respond variably, but overall positively, to increasing CO2 concentrations, generating negative feedbacks to climate change.
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Affiliation(s)
- Carmen C Zayas-Santiago
- Department of Ocean, Earth & Atmospheric Sciences, Old Dominion University, Norfolk, VA, 23429, USA.
| | - Albert Rivas-Ubach
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, WA, 99352, USA
| | - Li-Jung Kuo
- Marine Sciences Laboratory, Pacific Northwest National Laboratory, 1529 W. Sequim Bay Rd., Sequim, WA, 98382, USA
| | - Nicholas D Ward
- Marine Sciences Laboratory, Pacific Northwest National Laboratory, 1529 W. Sequim Bay Rd., Sequim, WA, 98382, USA.,School of Oceanography, University of Washington, Seattle, WA, 98105, USA
| | - Richard C Zimmerman
- Department of Ocean, Earth & Atmospheric Sciences, Old Dominion University, Norfolk, VA, 23429, USA
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15
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Gong S, Jin X, Xiao Y, Li Z. Ocean Acidification and Warming Lead to Increased Growth and Altered Chloroplast Morphology in the Thermo-Tolerant Alga Symbiochlorum hainanensis. FRONTIERS IN PLANT SCIENCE 2020; 11:585202. [PMID: 33281847 PMCID: PMC7705064 DOI: 10.3389/fpls.2020.585202] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/21/2020] [Indexed: 05/03/2023]
Abstract
Ocean acidification and warming affect the growth and predominance of algae. However, the effects of ocean acidification and warming on the growth and gene transcription of thermo-tolerant algae are poorly understood. Here we determined the effects of elevated temperature (H) and acidification (A) on a recently discovered coral-associated thermo-tolerant alga Symbiochlorum hainanensis by culturing it under two temperature settings (26.0 and 32.0°C) crossed with two pH levels (8.16 and 7.81). The results showed that the growth of S. hainanensis was positively affected by H, A, and the combined treatment (AH). However, no superimposition effect of H and A on the growth of S. hainanensis was observed under AH. The analysis of chlorophyll fluorescence, pigment content, and subcellular morphology indicated that the chloroplast morphogenesis (enlargement) along with the increase of chlorophyll fluorescence and pigment content of S. hainanensis might be a universal mechanism for promoting the growth of S. hainanensis. Transcriptomic profiles revealed the effect of elevated temperature on the response of S. hainanensis to acidification involved in the down-regulation of photosynthesis- and carbohydrate metabolism-related genes but not the up-regulation of genes related to antioxidant and ubiquitination processes. Overall, this study firstly reports the growth, morphology, and molecular response of the thermo-tolerant alga S. hainanensis to future climate changes, suggesting the predominance of S. hainanensis in its associated corals and/or coral reefs in the future.
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Affiliation(s)
- Sanqiang Gong
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Xuejie Jin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Yilin Xiao
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Zhiyong Li,
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16
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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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17
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Shah Mohammadi N, Buapet P, Pernice M, Signal B, Kahlke T, Hardke L, Ralph PJ. Transcriptome profiling analysis of the seagrass, Zostera muelleri under copper stress. MARINE POLLUTION BULLETIN 2019; 149:110556. [PMID: 31546108 DOI: 10.1016/j.marpolbul.2019.110556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 08/09/2019] [Accepted: 08/27/2019] [Indexed: 06/10/2023]
Abstract
Copper (Cu) in an essential trace metal but it can also contaminate coastal waters at high concentrations mainly from agricultural run-off and mining activities which are detrimental to marine organisms including seagrasses. The molecular mechanisms driving Cu toxicity in seagrasses are not clearly understood yet. Here, we investigated the molecular responses of the Australian seagrass, Z. muelleri at the whole transcriptomic level after 7 days of exposure to 250 μg Cu L-1 and 500 μg Cu L-1. The leaf-specific whole transcriptome results showed a concentration-dependent disturbance in chloroplast function, regulatory stress responses and defense mechanisms. This study provided new insights into the responses of seagrasses to trace metal stress and reports possible candidate genes which can be considered as biomarkers to improve conservation and management of seagrass meadows.
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Affiliation(s)
- Nasim Shah Mohammadi
- University of Technology Sydney (UTS), Climate Change Cluster (C3), Broadway, Ultimo, NSW 2007, Australia
| | - Pimchanok Buapet
- Plant Physiology Laboratory, Department of Biology, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand; Coastal Oceanography and Climate Change Research Center, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Mathieu Pernice
- University of Technology Sydney (UTS), Climate Change Cluster (C3), Broadway, Ultimo, NSW 2007, Australia.
| | - Bethany Signal
- University of Technology Sydney (UTS), Climate Change Cluster (C3), Broadway, Ultimo, NSW 2007, Australia
| | - Tim Kahlke
- University of Technology Sydney (UTS), Climate Change Cluster (C3), Broadway, Ultimo, NSW 2007, Australia
| | - Leo Hardke
- School of Earth and Environmental Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter J Ralph
- University of Technology Sydney (UTS), Climate Change Cluster (C3), Broadway, Ultimo, NSW 2007, Australia
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18
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Oscar MA, Barak S, Winters G. The Tropical Invasive Seagrass, Halophila stipulacea, Has a Superior Ability to Tolerate Dynamic Changes in Salinity Levels Compared to Its Freshwater Relative, Vallisneria americana. FRONTIERS IN PLANT SCIENCE 2018; 9:950. [PMID: 30022993 PMCID: PMC6040085 DOI: 10.3389/fpls.2018.00950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/12/2018] [Indexed: 05/30/2023]
Abstract
The tropical seagrass species, Halophila stipulacea, originated from the Indian Ocean and the Red Sea, subsequently invading the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest in understanding this species' capacity to adapt to new conditions. One approach to understanding the natural tolerance of a plant is to compare the tolerant species with a closely related non-tolerant species. We compared the physiological responses of H. stipulacea exposed to different salinities, with that of its nearest freshwater relative, Vallisneria americana. To achieve this goal, H. stipulacea and V. americana plants were grown in dedicated microcosms, and exposed to the following salt regimes: (i) H. stipulacea: control (40 PSU, practical salinity units), hyposalinity (25 PSU) and hypersalinity (60 PSU) for 3 weeks followed by a 4-week recovery phase (back to 40 PSU); (ii) V. americana: control (1 PSU), and hypersalinity (12 PSU) for 3 weeks, followed by a 4-week recovery phase (back to 1 PSU). In H. stipulacea, leaf number and chlorophyll content showed no significant differences between control plants and plants under hypo and hypersalinities, but a significant decrease in leaf area under hypersalinity was observed. In addition, compared with control plants, H. stipulacea plants exposed to hypo and hypersalinity were found to have reduced below-ground biomass and C/N ratios, suggesting changes in the allocation of resources in response to both stresses. There was no significant effect of hypo/hypersalinity on dark-adapted quantum yield of photosystem II (Fv/Fm) suggesting that H. stipulacea photochemistry is resilient to hypo/hypersalinity stress. In contrast to the seagrass, V. americana exposed to hypersalinity displayed significant decreases in above-ground biomass, shoot number, leaf number, blade length and Fv/Fm, followed by significant recoveries of all these parameters upon return of the plants to non-saline control conditions. These data suggest that H. stipulacea shows remarkable tolerance to both hypo and hypersalinity. Resilience to a relatively wide range of salinities may be one of the traits explaining the invasive nature of this species in the Mediterranean and Caribbean Seas.
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Affiliation(s)
- Michelle A. Oscar
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Dead-Sea & Arava Science Center, Neve Zohar, Israel
| | - Simon Barak
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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19
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Molecular level responses to chronic versus pulse nutrient loading in the seagrass Posidonia oceanica undergoing herbivore pressure. Oecologia 2018; 188:23-39. [PMID: 29845353 DOI: 10.1007/s00442-018-4172-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/20/2018] [Indexed: 12/31/2022]
Abstract
Seagrasses are key marine foundation species, currently declining due to the compounded action of global and regional anthropogenic stressors. Eutrophication has been associated with seagrass decline, while grazing has been traditionally considered to be a natural disturbance with a relatively low impact on seagrasses. In the recent years, this assumption has been revisited. Here, by means of a 16-month field-experiment, we investigated the molecular mechanisms driving the long-term response of Posidonia oceanica to the combination of nutrient enrichment, either as a chronic (press) or pulse disturbance, and herbivory. Changes in expression levels of 19 target genes involved in key steps of photosynthesis, nutrient assimilation, chlorophyll metabolism, oxidative-stress response and plant defense were evaluated through reverse transcription-quantitative polymerase chain reaction (RT-qPCR). High herbivore pressure affected the molecular response of P. oceanica more dramatically than did enhanced nutrient levels, altering the expression of genes involved in plant tolerance and resistance traits, such as photosynthesis and defense mechanisms. Genes involved in carbon fixation and N assimilation modulated the response of plants to high nutrient levels. Availability of resources seems to modify P. oceanica response to herbivory, where the upregulation of a nitrate transporter gene was accompanied by the decline in the expression of nitrate reductase in the leaves, suggesting a change in plant-nutrient allocation strategy. Finally, press and pulse fertilizations altered nitrate uptake and reduction-related genes in opposite ways, suggesting that taking into account the temporal regime of nutrient loading is important to assess the physiological response of seagrasses to eutrophication.
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20
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Sablok G, Hayward RJ, Davey PA, Santos RP, Schliep M, Larkum A, Pernice M, Dolferus R, Ralph PJ. SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants. Sci Rep 2018; 8:2749. [PMID: 29426939 PMCID: PMC5807536 DOI: 10.1038/s41598-017-18782-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 12/11/2017] [Indexed: 12/04/2022] Open
Abstract
Seagrasses and aquatic plants are important clades of higher plants, significant for carbon sequestration and marine ecological restoration. They are valuable in the sense that they allow us to understand how plants have developed traits to adapt to high salinity and photosynthetically challenged environments. Here, we present a large-scale phylogenetically profiled transcriptomics repository covering seagrasses and aquatic plants. SeagrassDB encompasses a total of 1,052,262 unigenes with a minimum and maximum contig length of 8,831 bp and 16,705 bp respectively. SeagrassDB provides access to 34,455 transcription factors, 470,568 PFAM domains, 382,528 prosite models and 482,121 InterPro domains across 9 species. SeagrassDB allows for the comparative gene mining using BLAST-based approaches and subsequent unigenes sequence retrieval with associated features such as expression (FPKM values), gene ontologies, functional assignments, family level classification, Interpro domains, KEGG orthology (KO), transcription factors and prosite information. SeagrassDB is available to the scientific community for exploring the functional genic landscape of seagrass and aquatic plants at: http://115.146.91.129/index.php.
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Affiliation(s)
- Gaurav Sablok
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia.
| | - Regan J Hayward
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Peter A Davey
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Rosiane P Santos
- Laboratório de Recursos Genéticos, Universidade Federal de São João Del-Rei, Campus CTAN, São João Del Rei, Minas Gerais, 36307-352, Brazil
| | - Martin Schliep
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Anthony Larkum
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Mathieu Pernice
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia
| | - Rudy Dolferus
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Peter J Ralph
- Climate Change Cluster (C3), University of Technology Sydney, PO Box 123 Broadway, NSW 2007, Australia.
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21
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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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