Genomewide transcriptional reprogramming in the seagrass Cymodocea nodosa under experimental ocean acidification

The metabolic network response and tolerance mechanism of Thalassia hemprichii under high sulfide based on widely targeted metabolome and transcriptome

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.

Diverse RNA viruses discovered in multiple seagrass species

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.

Thermo-priming triggers species-specific physiological and transcriptome responses in Mediterranean seagrasses

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.

Transcriptomic profiles and diagnostic biomarkers in the Mediterranean seagrasses Posidonia oceanica and Cymodocea nodosa reveal mechanistic insights of adaptative strategies upon desalination brine stress

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.

Ocean acidification impairs seagrass performance under thermal stress in shallow and deep water

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.

Single-molecule real-time sequencing of the full-length transcriptome of Halophila beccarii

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.

2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation

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.

Daily Regulation of Key Metabolic Pathways in Two Seagrasses Under Natural Light Conditions

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.

Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress

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.

Integrating Transcriptomics and Metabolomics to Characterize Metabolic Regulation to Elevated CO2 in Chlamydomonas Reinhardtii

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.

Leaf proteome modulation and cytological features of seagrass Cymodocea nodosa in response to long-term high CO2 exposure in volcanic vents

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.

m6A RNA Methylation in Marine Plants: First Insights and Relevance for Biological Rhythms

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.

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L

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.

Metabolic Profiling Reveals Biochemical Pathways Responsible for Eelgrass Response to Elevated CO2 and Temperature

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.

Ocean Acidification and Warming Lead to Increased Growth and Altered Chloroplast Morphology in the Thermo-Tolerant Alga Symbiochlorum hainanensis

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.

Elevated trace elements in sediments and seagrasses at CO2 seeps

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.

Transcriptome profiling analysis of the seagrass, Zostera muelleri under copper stress

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.

The Tropical Invasive Seagrass, Halophila stipulacea, Has a Superior Ability to Tolerate Dynamic Changes in Salinity Levels Compared to Its Freshwater Relative, Vallisneria americana

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.

Molecular level responses to chronic versus pulse nutrient loading in the seagrass Posidonia oceanica undergoing herbivore pressure

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.

SeagrassDB: An open-source transcriptomics landscape for phylogenetically profiled seagrasses and aquatic plants

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.

Antioxidant response to heat stress in seagrasses. A gene expression study

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.