Phenotypic plasticity under rapid global changes: The intrinsic force for future seagrasses survival

Mass flowering and unprecedented extended pseudovivipary in seagrass (Posidonia oceanica) after a Marine Heat Wave

Seagrasses are marine flowering plants that create critical coastal ecosystems and are threatened by warming. Clonal expansion is generally the dominant strategy for meadow recovery, while sexual reproduction strongly differs among species (e.g., monoecious and diecious species, some creating seed banks, viviparous seedlings). In 2022, the Western Mediterranean underwent unprecedented warming, and, associated with it, we observed flowering (100 %) across 11 Posidonia oceanica meadows in Mallorca, Balearic Islands. Furthermore, 64 % of the sites also exhibited pseudovivipary, an extremely rare phenomenon in angiosperms whereby plantlets replace sexual reproductive structures, producing clones of the maternal plant. Our results support the notion that P. oceanica flowering and pseudovivipary (genetically confirmed) are triggered by warming, never before being pseudovivipary reported across multiple sites in a marine plant. Considering the negative impacts that warming can have on seagrasses, existence of widespread pseudovivipary is a critical aspect to consider for understanding mechanisms of resilience in seagrasses.

An epigenetic toolbox for conservation biologists

Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.

The resilience of transplanted seagrass traits encourages detection of restoration success

Restoration of coastal ecosystems, particularly those dominated by seagrasses, has become a priority to recover the important ecosystem services they provide. However, assessing restoration outcomes as a success or failure remains still difficult, probably due to the unique features of seagrass species and the wide portfolio of practices used on transplanting actions. Here, several traits (maximum leaf length, number of leaves, leaf growth rate per shoot, and leaf elemental carbon and nitrogen contents) of transplanted seagrass Posidonia oceanica were compared to reference meadows in five sites of Western Mediterranean Sea in which restoration were completed in different times. Results have evidenced the resilience of transplanted P. oceanica shoots within a few years since restoration, as traits between treatments changed depending on the elapsed time since settlement. The highlighted stability of the restoration time effect suggests that the recovery of the plants is expected in four years after transplanting.

Exploring priming strategies to improve stress resilience of Posidonia oceanica seedlings

Seagrasses' ability to store information after exposure to stress (i.e. stress memory) and to better respond to further stress (i.e. priming) have recently been observed, although the temporal persistence of the memory and the mechanisms for priming induction remain to be defined. Here, we explored three priming strategies in Posidonia oceanica seedlings, each inducing a different level of stress, for temperature and salinity. We investigated changes in morphometry, growth rate and biomass between primed and non-primed seedlings. The results showed similar behaviour of seedlings when exposed to an acute stress event, regardless of whether they had been primed or not and of the priming strategy received. This opens the debate on the level of stress necessary for inducing a priming status and the persistence of the stress memory in P. oceanica seedlings. Although no priming-induced stress resistance was observed, seedlings showed unexpectedly high resilience to extreme levels of both abiotic stressors.

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.

Marine heatwaves recurrence aggravates thermal stress in the surfgrass Phyllospadix scouleri

The surfgrass Phyllospadix scouleri grows in highly productive meadows along the Pacific coast of North America. This region has experienced increasingly severe marine heatwaves (MHWs) in recent years. Our study evaluated the impact of consecutive MHWs, simulated in mesocosms, on essential ecophysiological features of P. scouleri. Overall, our findings show that the plants' overall physiological status has been progressively declining. Interestingly, the indicators of physiological stress in photosynthesis only showed up once the initial heat exposure stopped (i.e., during the recovery period). The warming caused increased oxidative damage and a decrease in nitrate uptake rates. However, the levels of non-structural carbohydrates and relative growth rates were not affected. Our findings emphasize the significance of incorporating recovery periods in this type of study as they expose delayed stress responses. Furthermore, experiencing consecutive intense MHWs can harm surfgrasses over time, compromising the health of their meadows and the services they offer to the ecosystem.

Induced responses contribute to rapid adaptation of Spirodela polyrhiza to herbivory by Lymnaea stagnalis

Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolve populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail), testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We show that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggest that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.

Calm after the storm? Similar patterns of genetic variation in a riverine foundation species before and after severe disturbance

In summer 2011, Tropical storms Lee and Irene caused an estimated 90% decline of the submersed aquatic plant Vallisneria americana Michx. (Hydrocharitaceae) in the Hudson River of New York (USA). To understand the genetic impact of such large-scale demographic losses, we compared diversity at 10 microsatellite loci in 135 samples collected from five sites just before the storms with 239 shoots collected from nine sites 4 years after. Although 80% of beds sampled in 2011 lacked V. americana in 2015, we found similar genotypic and genetic diversity and effective population sizes in pre-storm versus post-storm sites. These similarities suggest that despite local extirpations concentrated at the upstream end of the sampling area, V. americana was regionally resistant to genetic losses. Similar geographically based structure among sites in both sampling periods suggested that cryptic local refugia at previously occupied sites facilitated re-expansion after the storms. However, this apparent resistance to disturbance may lead to a false sense of security. Low effective population sizes and high clonality in both time periods suggest that V. americana beds were already small and had high frequency of asexual reproduction before the storms. Dispersal was not sufficient to recolonize more isolated sites that had been extirpated. Chronic low diversity and reliance on asexual reproduction for persistence can be risky when more frequent and intense storms are paired with ongoing anthropogenic stressors. Monitoring genetic diversity along with extent and abundance of V. americana will give a more complete picture of long-term potential for resilience.

Evaluation of species thermal sensitivity with individual-based physiological performance

Ignoring intraspecific variations can prevent us from accurately assessing species' thermal sensitivity to global warming. Individual-based physiological performance provides a feasible solution to depict species' thermal sensitivity using a bottom-up approach. We measured the cardiac performance of intertidal bivalves (1159 individuals from multiple populations of six bivalves), determined the upper thermal limit of each individual, calculated the proportions of individuals suffering sublethal/lethal heat stress, and mapped sensitive regions to high temperatures. Results showed that high inter-individual variations of physiological performance existed in levels of populations and species, and species' thermal sensitivity was positively related to the intraspecific variations of heat tolerance. This bottom-up approach scaled up from individual, population to species emphasizes the importance of individual-based physiology performance in assessing thermal sensitivity across different hierarchical levels and enables better evaluating and forecasting of species responses to global warming.

Benzophenone-3 does not Cause Oxidative Stress or B-esterase Inhibition During Embryo Development of Octopus maya (Voss and Solís Ramírez, 1966)

Benzophenone-3 (BP-3) is an active ingredient in sunscreen lotions and personal-care products that protects against the damaging effects of ultraviolet rays. Given its worldwide dissemination, it has been linked with harmful effects on aquatic biota; however, its impact is not fully understood calling for further studies. To understand the impacts on an important economically and ecologically species, we evaluated the toxicity of BP-3 during the embryonic development of Octopus maya. Embryos were exposed to increasing concentrations of up to 500 µg BP-3/L until hatching. Antioxidant enzyme activities, oxidative-stress indicators, and B-esterases activities were measured at different developmental phases (organogenesis, activation, and growth). There were no significant differences between treatments, suggesting the lack of production of toxic metabolites that may be related to a protective chorion, an underdeveloped detoxification system, and the experimental conditions that limited phototoxicity.

Microbial community changes correlate with impaired host fitness of Aurelia aurita after environmental challenge

Climate change globally endangers certain marine species, but at the same time, such changes may promote species that can tolerate and adapt to varying environmental conditions. Such acclimatization can be accompanied or possibly even be enabled by a host's microbiome; however, few studies have so far directly addressed this process. Here we show that acute, individual rises in seawater temperature and salinity to sub-lethal levels diminished host fitness of the benthic Aurelia aurita polyp, demonstrated by up to 34% reduced survival rate, shrinking of the animals, and almost halted asexual reproduction. Changes in the fitness of the polyps to environmental stressors coincided with microbiome changes, mainly within the phyla Proteobacteria and Bacteroidota. The absence of bacteria amplified these effects, pointing to the benefit of a balanced microbiota to cope with a changing environment. In a future ocean scenario, mimicked by a combined but milder rise of temperature and salinity, the fitness of polyps was severely less impaired, together with condition-specific changes in the microbiome composition. Our results show that the effects on host fitness correlate with the strength of environmental stress, while salt-conveyed thermotolerance might be involved. Further, a specific, balanced microbiome of A. aurita polyps supports the host's acclimatization. Microbiomes may provide a means for acclimatization, and microbiome flexibility can be a fundamental strategy for marine animals to adapt to future ocean scenarios and maintain biodiversity and ecosystem functioning.

Increasing temperature-driven changes in life history traits and gene expression of an Antarctic tardigrade species

The Antarctic region has been experiencing some of the planet's strongest climatic changes, including an expected increase of the land temperature. The potential effects of this warming trend will lead ecosystems to a risk of losing biodiversity. Antarctic mosses and lichens host different microbial groups, micro-arthropods and meiofaunal organisms (e.g., tardigrades, rotifers). The eutardigrade Acutuncus antarcticus is considered a model animal to study the effect of increasing temperature due to global warming on Antarctic terrestrial communities. In this study, life history traits and fitness of this species are analyzed by rearing specimens at two different and increasing temperatures (5°C vs. 15°C). Moreover, the first transcriptome analysis on A. antarcticus is performed, exposing adult animals to a gradual increase of temperature (5°C, 10°C, 15°C, and 20°C) to find differentially expressed genes under short- (1 day) and long-term (15 days) heat stress. Acutuncus antarcticus specimens reared at 5°C live longer (maximum life span: 686 days), reach sexual maturity later, lay more eggs (which hatch in longer time and in lower percentage) compared with animals reared at 15°C. The fitness decreases in animals belonging to the second generation at both rearing temperatures. The short-term heat exposure leads to significant changes at transcriptomic level, with 67 differentially expressed genes. Of these, 23 upregulated genes suggest alterations of mitochondrial activity and oxido-reductive processes, and two intrinsically disordered protein genes confirm their role to cope with heat stress. The long-term exposure induces alterations limited to 14 genes, and only one annotated gene is upregulated in response to both heat stresses. The decline in transcriptomic response after a long-term exposure indicates that the changes observed in the short-term are likely due to an acclimation response. Therefore, A. antarcticus could be able to cope with increasing temperature over time, including the future conditions imposed by global climate change.

Differential Morpho-Physiological and Biochemical Responses of Duckweed Clones from Saudi Arabia to Salinity

Salinity affects the morphological, physiological, and biochemical characteristics of several plant species. The current study was conducted to investigate differential salt tolerance potentials among ten duckweed clones under different salt-stress conditions. Morphological and physiological parameters, including fronds length, fronds number, root length, root number, Na+/K+, chlorophyll, proline contents, and fresh harvest weight, were recorded for each of the ten duckweed clones collected from different Saudi Arabia regions. Additionally, the expression patterns of seven salt-related genes were monitored in a salt-tolerant duckweed genotype. The results show that the Madinah-2 (Spirodela polyryiza) and Al-Qassim (Landoltia punctata) clones presented higher performances for all the tested morphological and physiological parameters compared to other genotypes under salt-stress conditions. At concentrations greater than 150 mM NaCl, these aforementioned traits were affected for all the genotypes tested, except Madinah-2 (S. polyryiza) and Al-Qassim (L. punctata) clones, both of which exhibited high tolerance behavior under high salt conditions (200 mM and 250 mM NaCl). The principal component analysis (PCA) showed that the first five principal components accounted for 94.8% of the total variance among the studied traits. Morphological and physiological traits are the major portions of PC1. Moreover, the expression pattern analysis of NHX, BZIP, ST, and KTrans transcript revealed their upregulation in the Al-Qassim clone under salt-stress conditions, suggesting that these genes play a role in this clone's tolerance to salt-induced stress. Overall, this study indicates that the Al-Qassim clone could be used in a brackish-water duckweed-based treatment program with a simultaneous provision of valuable plant biomass.

Relationships between phenotypic plasticity and epigenetic variation in two Caribbean Acropora corals

The plastic ability for a range of phenotypes to be exhibited by the same genotype allows organisms to respond to environmental variation and may modulate fitness in novel environments. Differing capacities for phenotypic plasticity within a population, apparent as genotype by environment interactions (GxE), can therefore have both ecological and evolutionary implications. Epigenetic gene regulation alters gene function in response to environmental cues without changes to the underlying genetic sequence and likely mediates phenotypic variation. DNA methylation is currently the most well described epigenetic mechanism and is related to transcriptional homeostasis in invertebrates. However, evidence quantitatively linking variation in DNA methylation with that of phenotype is lacking in some taxa, including reef-building corals. In this study, spatial and seasonal environmental variation in Bonaire, Caribbean Netherlands was utilized to assess relationships between physiology and DNA methylation profiles within genetic clones across different genotypes of Acropora cervicornis and A. palmata corals. The physiology of both species was highly influenced by environmental variation compared to the effect of genotype. GxE effects on phenotype were only apparent in A. cervicornis. DNA methylation in both species differed between genotypes and seasons and epigenetic variation was significantly related to coral physiological metrics. Furthermore, plastic shifts in physiology across seasons were significantly positively correlated with shifts in DNA methylation profiles in both species. These results highlight the dynamic influence of environmental conditions and genetic constraints on the physiology of two important Caribbean coral species. Additionally, this study provides quantitative support for the role of epigenetic DNA methylation in mediating phenotypic plasticity in invertebrates.

Signs of local adaptation by genetic selection and isolation promoted by extreme temperature and salinity in the Mediterranean seagrass Posidonia oceanica

Adaptation to local conditions is known to occur in seagrasses; however, knowledge of the genetic basis underlying this phenomenon remains scarce. Here, we analysed Posidonia oceanica from six sites within and around the Stagnone di Marsala, a semi-enclosed coastal lagoon where salinity and temperature exceed the generally described tolerance thresholds of the species. Sea surface temperatures (SSTs) were measured and plant samples were collected for the assessment of morphology, flowering rate and for screening genome-wide polymorphisms using double digest restriction-site-associated DNA sequencing. Results demonstrated more extreme SSTs and salinity levels inside the lagoon than the outer lagoon regions. Morphological results showed significantly fewer and shorter leaves and reduced rhizome growth of P. oceanica from the inner lagoon and past flowering events were recorded only for a meadow farthest away from the lagoon. Using an array of 51,329 single nucleotide polymorphisms, we revealed a clear genetic structure among the study sites and confirmed the genetic isolation and high clonality of the innermost site. In all, 14 outlier loci were identified and annotated with several proteins including those relate to plant stress response, protein transport and regulators of plant-specific developmental events. Especially, five outlier loci showed maximum allele frequency at the innermost site, likely reflecting adaptation to the extreme temperature and salinity regimes, possibly due to the selection of more resistant genotypes and the progressive restriction of gene flow. Overall, this study helps us to disentangle the genetic basis of seagrass adaptation to local environmental conditions and may support future works on assisted evolution in seagrasses.

Design, execution, and interpretation of plant RNA-seq analyses

Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences. We discuss the importance of experimental design in RNA-seq, including considerations for sampling and replication, to avoid pitfalls and wasted resources. Approaches for processing RNA-seq data include quality control and counting features, and we describe common approaches and variations. Though differential gene expression analysis is the most common analysis of RNA-seq data, we review multiple methods for assessing gene expression, including detecting allele-specific gene expression and building co-expression networks. With the production of more RNA-seq data, strategies for integrating these data into genetic mapping pipelines is of increased interest. Finally, special considerations for RNA-seq analysis and interpretation in plants are needed, due to the high genome complexity common across plants. By incorporating informed decisions throughout an RNA-seq experiment, we can increase the knowledge gained.

Gene co-expression network analysis for the selection of candidate early warning indicators of heat and nutrient stress in Posidonia oceanica

The continuous worldwide seagrasses decline calls for immediate actions in order to preserve this precious marine ecosystem. The main stressors that have been linked with decline in seagrasses are 1) the increasing ocean temperature due to climate change and 2) the continuous inputs of nutrients (eutrophication) associated with coastal human activities. To avoid the loss of seagrass populations, an "early warning" system is needed. We used Weighed Gene Co-expression Network Analysis (WGCNA), a systems biology approach, to identify potential candidate genes that can provide an early warning signal of stress in the Mediterranean iconic seagrass Posidonia oceanica, anticipating plant mortality. Plants were collected from both eutrophic (EU) and oligotrophic (OL) environments and were exposed to thermal and nutrient stress in a dedicated mesocosm. By correlating the whole-genome gene expression after 2-weeks exposure with the shoot survival percentage after 5-weeks exposure to stressors, we were able to identify several transcripts that indicated an early activation of several biological processes (BP) including: protein metabolic process, RNA metabolic process, organonitrogen compound biosynthetic process, catabolic process and response to stimulus, which were shared among OL and EU plants and among leaf and shoot apical meristem (SAM), in response to excessive heat and nutrients. Our results suggest a more dynamic and specific response of the SAM compared to the leaf, especially the SAM from plants coming from a stressful environment appeared more dynamic than the SAM from a pristine environment. A vast list of potential molecular markers is also provided that can be used as targets to assess field samples.

Experimental DNA Demethylation Reduces Expression Plasticity and Thermal Tolerance in Pacific Oysters

Increasing seawater temperatures pose a great threat to marine organisms, especially those settled in fluctuating intertidal areas. DNA methylation, which can be induced by environmental variation, can influence gene expression and mediate phenotypic plasticity. However, the regulatory mechanisms of DNA methylation in gene expression-mediated adaptation to environmental stress have rarely been elucidated. In this study, DNA demethylation experiments were conducted on a typical intertidal species, the Pacific oyster (Crassostrea gigas), to determine the direct role of DNA methylation in regulating gene expression and adaptability under thermal stress. The global methylation level and the expression level of DNA methyltransferases (DNMT1, DNMT3a) showed an accordant variation trend under high temperatures, supporting that the genomic methylation status was catalyzed by DNMTs. DNA methylation inhibitor 5-Azacytidine (5-Aza) effectively inhibited DNA methylation level and decreased methylation plasticity at the 6th hour in thermal conditions. In total, 88 genes were identified as candidate DNA methylation-regulated thermal response genes; they exhibited reduced expression plasticity in response to heat stress, possibly caused by the decreased methylation plasticity. Post-heat shock, the thermal tolerance indicated by the survival curve was reduced when oysters were pretreated with 5-Aza, meaning that DNA demethylation negatively affected thermal adaptation in oysters. This study provides direct evidence for the crucial role of DNA methylation in mediating stress adaptation in marine invertebrates and contributes to the theoretical foundations underlying marine resource conservation and aquaculture.

A trait-based framework for seagrass ecology: Trends and prospects

In the last three decades, quantitative approaches that rely on organism traits instead of taxonomy have advanced different fields of ecological research through establishing the mechanistic links between environmental drivers, functional traits, and ecosystem functions. A research subfield where trait-based approaches have been frequently used but poorly synthesized is the ecology of seagrasses; marine angiosperms that colonized the ocean 100M YA and today make up productive yet threatened coastal ecosystems globally. Here, we compiled a comprehensive trait-based response-effect framework (TBF) which builds on previous concepts and ideas, including the use of traits for the study of community assembly processes, from dispersal and response to abiotic and biotic factors, to ecosystem function and service provision. We then apply this framework to the global seagrass literature, using a systematic review to identify the strengths, gaps, and opportunities of the field. Seagrass trait research has mostly focused on the effect of environmental drivers on traits, i.e., "environmental filtering" (72%), whereas links between traits and functions are less common (26.9%). Despite the richness of trait-based data available, concepts related to TBFs are rare in the seagrass literature (15% of studies), including the relative importance of neutral and niche assembly processes, or the influence of trait dominance or complementarity in ecosystem function provision. These knowledge gaps indicate ample potential for further research, highlighting the need to understand the links between the unique traits of seagrasses and the ecosystem services they provide.

Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms

Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals' response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies nonzero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, result in flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experiments in silico. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral, or no plasticity, without any additional knowledge of the traits assessed and species' biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopod Idotea balthica sampled from two geographical locations with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments or correlated to fitness.

DNA methylation dynamics in a coastal foundation seagrass species under abiotic stressors

DNA methylation (DNAm) has been intensively studied in terrestrial plants in response to environmental changes, but its dynamic changes in a temporal scale remain unexplored in marine plants. The seagrass Posidonia oceanica ranks among the slowest-growing and longest-living plants on Earth, and is particularly vulnerable to sea warming and local anthropogenic pressures. Here, we analysed the dynamics of DNAm changes in plants collected from coastal areas differentially impacted by eutrophication (i.e. oligotrophic, Ol; eutrophic, Eu) and exposed to abiotic stressors (nutrients, temperature increase and their combination). Levels of global DNAm (% 5-mC) and the expression of key genes involved in DNAm were assessed after one, two and five weeks of exposure. Results revealed a clear differentiation between plants, depending on environmental stimuli, time of exposure and plants' origin. % 5-mC levels were higher during the initial stress exposure especially in Ol plants, which upregulated almost all genes involved in DNAm. Contrarily, Eu plants showed lower expression levels, which increased under chronic exposure to stressors, particularly to temperature. These findings show that DNAm is dynamic in P. oceanica during stress exposure and underlined that environmental epigenetic variations could be implicated in the regulation of acclimation and phenotypic differences depending on local conditions.

Plant and Meadow Structure Characterisation of Posidonia oceanica in Its Westernmost Distribution Range

Posidonia oceanica is an endemic seagrass species from the Mediterranean Sea that provides critical ecological services to coastal environments. This species is distributed from the Turkish to the Spanish coast, where its westernmost record was documented in Punta Chullera, Malaga (36°18′36.45′′ N, 5°14′54.31′′ W). Nevertheless, previous studies suggested that its distribution was even further west, although these populations were never described. In this study, we documented and characterised the only known P. oceanica population on the coast of Cadiz, in Cala Sardina (36°18′38.80′′ N, 5°15′15.13′′ W). The newly documented population of P. oceanica presented a fragmented structure, consisting of nine patches found in a rocky shallow area surrounded by the invasive algae Rugulopteryx okamurae, with a total size of 61.14 m2. Shoots had a relatively small size (21.0 ± 2.9 cm) in comparison with centrally-distributed populations. The relatively small size of the plants, alongside the observed low shoot density (437 ± 42 shoots m−2) and leaf area index (4.8 ± 0.7 m2 m−2), may indicate that this meadow could be exposed to sub-optimal environmental conditions for plant development. By contrast, the meadow showed relatively high production rates (0.03 ± 0.01 leaf day−1 shoot−1) in comparison with other Mediterranean populations. The percentage of carbon in plant leaves was 38.73 ± 1.38%, while the nitrogen and C/N were 1.38 ± 0.37% and 29.93 ± 6.57, respectively. The documentation of this meadow extends the distribution of this species to the Mediterranean coast of Cadiz, making this region the place with the highest seagrass biodiversity (four species) in the Iberian Peninsula, and potentially in Europe. This exploratory study provides a baseline to examine the potential effects of climate change, anthropogenic disturbances or the presence of invasive species.

Advances in understanding multilevel responses of seagrasses to hypersalinity

Human- and nature-induced hypersaline conditions in coastal systems can lead to profound alterations of the structure and vitality of seagrass meadows and their socio-ecological benefits. In the last two decades, recent research efforts (>50 publications) have contributed significantly to unravel the physiological basis underlying the seagrass-hypersalinity interactions, although most (∼70%) are limited to few species (e.g. Posidonia oceanica, Zostera marina, Thalassia testudinum, Cymodocea nodosa). Variables related to photosynthesis and carbon metabolism are among the most prevalent in the literature, although other key metabolic processes such as plant water relations and responses at molecular (i.e. gene expression) and ultrastructure level are attracting attention. This review emphasises all these latest insights, offering an integrative perspective on the interplay among biological responses across different functional levels (from molecular to clonal structure), and their interaction with biotic/abiotic factors including those related to climate change. Other issues such as the role of salinity in driving the evolutionary trajectory of seagrasses, their acclimation mechanisms to withstand salinity increases or even the adaptive properties of populations that have historically lived under hypersaline conditions are also included. The pivotal role of the costs and limits of phenotypic plasticity in the successful acclimation of marine plants to hypersalinity is also discussed. Finally, some lines of research are proposed to fill the remaining knowledge gaps.

Limited trait responses of a tropical seagrass to the combination of increasing pCO2 and warming

Understanding species-specific trait responses under future global change scenarios is of importance for conservation efforts and to make informed decisions within management projects. The combined and single effects of seawater acidification and warmer average temperature were investigated by means of the trait responses of Cymodocea serrulata, a tropical seagrass, under experimental conditions. After a 35 d exposure period, biochemical, morphological, and photo-physiological trait responses were measured. Overall, biochemical traits mildly responded under the individual exposure to high temperature and increasing pCO2 values. The response of C. serrulata was limited to a decrease in %C and an increase in the sucrose content in the rhizome under the high temperature treatment, 32 °C. This suggests that this temperature was lower than the maximum tolerance limit for this species. Increasing pCO2 levels increased %C in the rhizome, and also showed a significant increase in leaf δ13C values. The effects of all treatments were sublethal; however, small changes in their traits could affect the ecosystem services they provide. In particular, changes in tissue carbon concentrations may affect carbon storage capacity, one key ecosystem service. The simultaneous study of different types of trait responses contributes to establish a holistic framework of seagrass ecosystem health under climate change.

Collating evidence on the restoration efforts of the seagrass Posidonia oceanica: current knowledge and gaps

Seagrass meadows are important shallow coastal ecosystems due to their contribution to enhancing biodiversity, nutrient cycling, carbon burial, and sediment stabilisation, but the maintenance of their integrity has been threatened by several anthropogenic disturbances. Active restoration is considered a reliable strategy to enhance recovery of seagrass ecosystems, and decision making for correct seagrass restoration management requires relying on valuable information regarding the effectiveness of past restoration actions and experimental efforts. Previous experimental efforts and human-mediated active restoration actions of the slow growing seagrass Posidonia oceanica have been collated here by combining a literature systematic review and questionnaires consulting seagrass ecology experts. Overall, the poor consistency of the available information on P. oceanica restoration may be due to the wide portfolio of practices and methodologies used in different conditions, that supports the need of further field manipulative experiments in various environmental contexts to fill the identified knowledge gaps. The current situation requires an international, collaborative effort from scientists and stakeholders to jointly design the future strategy forward in identifying the best practices that lead to efficient restorations of P. oceanica habitat and functioning.

De novo assembly and annotation of the transcriptome of the endangered seagrass Zostera capensis: Insights from differential gene expression under thermal stress

Seagrasses are important marine ecosystem engineers but anthropogenic impacts and climate change have led to numerous population declines globally. In South Africa, Zostera capensis is endangered due to fragmented populations and heavy anthropogenic pressures on estuarine ecosystems that house the core of the populations. Addressing questions of how pressures such as climate change affect foundational species, including Z. capensis are crucial to supporting their conservation and underpin restoration efforts. Here we use ecological transcriptomics to study key functional responses of Z. capensis through quantification of gene expression after thermal stress and present the first reference transcriptome of Z. capensis. Four de novo reference assemblies (Trinity, IDBA-tran, RNAspades, SOAPdenovo) filtered through the EvidentialGene pipeline resulted in 153,755 transcripts with a BUSCO score of 66.1% for completeness. Differential expression analysis between heat stressed (32 °C for three days) and pre-warming plants identified genes involved in photosynthesis, oxidative stress, translation, metabolic and biosynthetic processes in the Z. capensis thermal stress response. This reference transcriptome is a significant contribution to the limited available genomic resources for Z. capensis and represents a vital tool for addressing questions around the species restoration and potential functional responses to warming marine environments.

Activating stress memory: eustressors as potential tools for plant breeding

Plants are continuously exposed to stress conditions, such that they have developed sophisticated and elegant survival strategies, which are reflected in their phenotypic plasticity, priming capacity, and memory acquisition. Epigenetic mechanisms play a critical role in modulating gene expression and stress responses, allowing malleability, reversibility, stability, and heritability of favourable phenotypes to enhance plant performance. Considering the urgency to improve our agricultural system because of going impacting climate change, potential and sustainable strategies rely on the controlled use of eustressors, enhancing desired characteristics and yield and shaping stress tolerance in crops. However, for plant breeding purposes is necessary to focus on the use of eustressors capable of establishing stable epigenetic marks to generate a transgenerational memory to stimulate a priming state in plants to face the changing environment.

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.

Photo-acclimatory thresholds anticipate sudden shifts in seagrass ecosystem state under reduced light conditions

Seagrass ecosystems usually respond in a nonlinear fashion to increasing pressures and environmental changes. Feedback mechanisms operating at the ecosystem level and involving multiple interactions among the seagrass meadow, its associated community and the physical environment are known to play a major role in such nonlinear responses. Phenotypic plasticity may also be important for buffering these ecological thresholds (i.e., regime shifts) as many physiological processes show nonlinear responses to gradual environmental changes, conferring the appearance of resistance before the effects at the organism and population levels are visible. However, the potential involvement of plant plasticity in driving catastrophic shifts in seagrass ecosystems has not yet been assessed. In this study, we conducted a manipulative 6-month light-gradient experiment in the field to capture nonlinearities of the physiological and population responses of the seagrass Cymodocea nodosa to gradual light reduction. The aim was to explore if and how the photo-acclimatory responses of shaded plants are translated to the population level and, hence, to the ecosystem level. Results showed that the seagrass population was rather stable under increasing shading levels through the activation of multilevel photo-acclimative responses, which are initiated with light reduction and modulated in proportion to shading intensity. The activation of photo-physiological and metabolic compensatory responses allowed shaded plants to sustain nearly constant plant productivity (metabolic carbon balance) along a range of shading levels before losing linearity and starting to decline. The species then activated plant- and meadow-scale photo-acclimative responses and drew on its energy reserves (rhizome carbohydrates) to confer additional population resilience. However, when the integration of all these buffering mechanisms failed to counterbalance the effects of extreme light limitation, the population collapsed, giving place to a phase shift from vegetated to bare sediments with catastrophic ecosystem outcomes. Our findings evidence that ecological thresholds in seagrass ecosystems under light limitation can be explained by the role of species' compensatory responses in modulating population-level responses. The thresholds of these plastic responses anticipate the sudden loss of seagrass meadows with the potential to be used as early warning indicators signalling the imminent collapse of the ecosystem, which is of great value for the real-world management of seagrass ecosystems.

The role of phenotypic plasticity in the establishment of range margins

It has been argued that adaptive phenotypic plasticity may facilitate range expansions over spatially and temporally variable environments. However, plasticity may induce fitness costs. This may hinder the evolution of plasticity. Earlier modelling studies examined the role of plasticity during range expansions of populations with fixed genetic variance. However, genetic variance evolves in natural populations. This may critically alter model outcomes. We ask: how does the capacity for plasticity in populations with evolving genetic variance alter range margins that populations without the capacity for plasticity are expected to attain? We answered this question using computer simulations and analytical approximations. We found a critical plasticity cost above which the capacity for plasticity has no impact on the expected range of the population. Below the critical cost, by contrast, plasticity facilitates range expansion, extending the range in comparison to that expected for populations without plasticity. We further found that populations may evolve plasticity to buffer temporal environmental fluctuations, but only when the plasticity cost is below the critical cost. Thus, the cost of plasticity is a key factor involved in range expansions of populations with the potential to express plastic response in the adaptive trait. This article is part of the theme issue 'Species' ranges in the face of changing environments (part I)'.

Ecological biomechanics of marine macrophytes

Macroalgae and seagrasses in coastal habitats are exposed to turbulent water currents and waves that deform them and can rip them off the substratum, but that also transport essential water-borne substances to them and disperse their propagules and wastes. Field studies of the physical environment, ecological interactions, and life history strategies of marine macrophytes reveal which aspects of their biomechanical performance are important to their success in different types of natural habitats and enable us to design ecologically relevant laboratory experiments to study biomechanical function. Morphology and tissue mechanical properties determine the hydrodynamic forces on macrophytes and their fate when exposed to those forces, but different mechanical designs can perform well in the same biophysical habitat. There is a trade-off between maximizing photosynthesis and minimizing breakage, and some macrophytes change their morphology in response to environmental cues. Water flow in marine habitats varies on a wide range of temporal and spatial scales, so diverse flow microhabitats can occur at the same site. Likewise, the size, shape, and tissue material properties of macrophytes change as they grow and age, so it is important to understand the different physical challenges met by macrophytes throughout their lives.

ITS DNA Barcoding Reveals That Halophila stipulacea Still Remains the Only Non-Indigenous Seagrass of the Mediterranean Sea

Non-indigenous species (NIS) are one of the major threats to the native marine ecosystems of the Mediterranean Sea. Halophila stipulacea was the only exotic seagrass of the Mediterranean until 2018, when small patches of a species morphologically identified as Halophila decipiens were reported in Salamina Island, Greece. Given the absence of reproductive structures during the identification and the taxonomic ambiguities known to lead to misidentifications on this genus, we reassessed the identity of this new exotic record using DNA barcoding (rbcL, matK and ITS) and the recently published taxonomic key. Despite their morphologic similarity to H. decipiens based on the new taxonomic key, the specimens showed no nucleotide differences with H. stipulacea specimens (Crete) for the three barcodes and clustered together on the ITS phylogenetic tree. Considering the high species resolution of the ITS region and the common morphological variability within the genus, the unequivocal genetic result suggests that the Halophila population found in Salamina Island most likely corresponds to a morphologically variant H. stipulacea. Our results highlight the importance of applying an integrated taxonomic approach (morphological and molecular) to taxonomically complex genera such as Halophila, in order to avoid overlooking or misreporting species range shifts, which is essential for monitoring NIS introductions.

Adaptation of Temperate Seagrass to Arctic Light Relies on Seasonal Acclimatization of Carbon Capture and Metabolism

Due to rising global surface temperatures, Arctic habitats are becoming thermally suitable for temperate species. Whether a temperate species can immigrate into an ice-free Arctic depends on its ability to tolerate extreme seasonal fluctuations in daylength. Thus, understanding adaptations to polar light conditions can improve the realism of models predicting poleward range expansions in response to climate change. Plant adaptations to polar light have rarely been studied and remain unknown in seagrasses. If these ecosystem engineers can migrate polewards, seagrasses will enrich biodiversity, and carbon capture potential in shallow coastal regions of the Arctic. Eelgrass (Zostera marina) is the most widely distributed seagrass in the northern hemisphere. As the only seagrass species growing as far north as 70°N, it is the most likely candidate to first immigrate into an ice-free Arctic. Here, we describe seasonal (and diurnal) changes in photosynthetic characteristics, and in genome-wide gene expression patterns under strong annual fluctuations of daylength. We compared PAM measurements and RNA-seq data between two populations at the longest and shortest day of the year: (1) a Mediterranean population exposed to moderate annual fluctuations of 10-14 h daylength and (2) an Arctic population exposed to high annual fluctuations of 0-24 h daylength. Most of the gene expression specificities of the Arctic population were found in functions of the organelles (chloroplast and mitochondrion). In winter, Arctic eelgrass conserves energy by repressing respiration and reducing photosynthetic energy fluxes. Although light-reactions, and genes involved in carbon capture and carbon storage were upregulated in summer, enzymes involved in CO2 fixation and chlorophyll-synthesis were upregulated in winter, suggesting that winter metabolism relies not only on stored energy resources but also on active use of dim light conditions. Eelgrass is unable to use excessive amounts of light during summer and demonstrates a significant reduction in photosynthetic performance under long daylengths, possibly to prevent photoinhibition constrains. Our study identified key mechanisms that allow eelgrass to survive under Arctic light conditions and paves the way for experimental research to predict whether and up to which latitude eelgrass can potentially migrate polewards in response to climate change.

Rapid adaptive responses of rosette-type macrophyte Vallisneria natans juveniles to varying water depths: The role of leaf trait plasticity

Rosette-type submerged macrophytes are widely distributed across a range of water depths in shallow lakes and play a key role in maintaining ecosystem structures and functions. However, little is known about the rapid adaptive responses of such macrophytes to variations in water depth, especially at the juvenile stage. Here, we conducted a short-term in situ mesocosm experiment, in which the juveniles of Vallisneria natans were exposed to a water depth gradient ranging from 20 to 360 cm. Twenty-two leaf-related traits were examined after 4 weeks of growth in a shallow lake. Most (18) traits of V. natans generally showed high plasticity in relation to water depth. Specifically, juveniles allocated more biomass to leaves and had higher specific leaf area, leaf length-to-width ratio, chlorophyll content, and carotenoids content in deep waters, displaying trait syndrome associated with high resource acquisition. In contrast, V. natans juveniles in shallow waters had higher leaf dry matter content, leaf soluble carbohydrate content, carotenoids per unit chlorophyll, and peroxidase activity, pertaining to resource conservation. Notably, underwater light intensity was found to be the key factor explaining the trait plasticity along the water depth gradient, and 1.30 mol photons m-2 d-1 (at 270 cm) could be the optimal irradiance level based on the total biomass of V. natans juveniles. The present study highlights the significance of leaf trait plasticity for rosette-type macrophytes in response to variations in water depth and sheds new light on the differences between trade-offs in deep- and shallow-water areas.

Trait gradients inform predictions of seagrass meadows changes to future warming

Comparing populations across temperature gradients can inform how global warming will impact the structure and function of ecosystems. Shoot density, morphometry and productivity of the seagrass Posidonia oceanica to temperature variation was quantified at eight locations in Sardinia (western Mediterranean Sea) along a natural sea surface temperature (SST) gradient. The locations are spanned for a narrow range of latitude (1.5°), allowing the minimization of the effect of eventual photoperiod variability. Mean SST predicted P. oceanica meadow structure, with increased temperature correlated with higher shoot density, but lower leaf and rhizome width, and rhizome biomass. Chlorophyll a (Chl-a) strongly impacted seagrass traits independent of SST. Disentangling the effects of SST and Chl-a on seagrass meadow shoot density revealed that they work independently, but in the same direction with potential synergism. Space-for-time substitution predicts that global warming will trigger denser seagrass meadows with slender shoots, fewer leaves, and strongly impact seagrass ecosystem. Future investigations should evaluate if global warming will erode the ecosystem services provided by seagrass meadows.

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.

Interindividual plasticity in metabolic and thermal tolerance traits from populations subjected to recent anthropogenic heating

To better understand temperature's role in the interaction between local evolutionary adaptation and physiological plasticity, we investigated acclimation effects on metabolic performance and thermal tolerance among natural Fundulus heteroclitus (small estuarine fish) populations from different thermal environments. Fundulus heteroclitus populations experience large daily and seasonal temperature variations, as well as local mean temperature differences across their large geographical cline. In this study, we use three populations: one locally heated (32°C) by thermal effluence (TE) from the Oyster Creek Nuclear Generating Station, NJ, and two nearby reference populations that do not experience local heating (28°C). After acclimation to 12 or 28°C, we quantified whole-animal metabolic (WAM) rate, critical thermal maximum (CTmax) and substrate-specific cardiac metabolic rate (CaM, substrates: glucose, fatty acids, lactate plus ketones plus ethanol, and endogenous (i.e. no added substrates)) in approximately 160 individuals from these three populations. Populations showed few significant differences due to large interindividual variation within populations. In general, for WAM and CTmax, the interindividual variation in acclimation response (log2 ratio 28/12°C) was a function of performance at 12°C and order of acclimation (12-28°C versus 28-12°C). CTmax and WAM were greater at 28°C than 12°C, although WAM had a small change (2.32-fold) compared with the expectation for a 16°C increase in temperature (expect 3- to 4.4-fold). By contrast, for CaM, the rates when acclimatized and assayed at 12 or 28°C were nearly identical. The small differences in CaM between 12 and 28°C temperature were partially explained by cardiac remodeling where individuals acclimatized to 12°C had larger hearts than individuals acclimatized to 28°C. Correlation among physiological traits was dependent on acclimation temperature. For example, WAM was negatively correlated with CTmax at 12°C but positively correlated at 28°C. Additionally, glucose substrate supported higher CaM than fatty acid, and fatty acid supported higher CaM than lactate, ketones and alcohol (LKA) or endogenous. However, these responses were highly variable with some individuals using much more FA than glucose. These findings suggest interindividual variation in physiological responses to temperature acclimation and indicate that additional research investigating interindividual may be relevant for global climate change responses in many species.

Intraspecific genetic variation matters when predicting seagrass distribution under climate change

Seagrasses play a vital role in structuring coastal marine ecosystems, but their distributional range and genetic diversity have declined rapidly in recent decades. To improve conservation of seagrass species, it is important to predict how climate change may impact their ranges. Such predictions are typically made with correlative species distribution models (SDMs), which can estimate a species' potential distribution under present and future climatic scenarios given species' presence data and climatic predictor variables. However, these models are typically constructed with species-level data, and thus ignore intraspecific genetic variability, which can give rise to populations with adaptations to heterogeneous climatic conditions. Here, we explore the link between intraspecific adaptation and niche differentiation in Thalassia hemprichii, a seagrass broadly distributed in the tropical Indo-Pacific Ocean and a crucial provider of habitat for numerous marine species. By retrieving and re-analysing microsatellite data from previous studies, we delimited two distinct phylogeographical lineages within the nominal species and found an intermediate level of differentiation in their multidimensional environmental niches, suggesting the possibility for local adaptation. We then compared projections of the species' habitat suitability under climate change scenarios using species-level and lineage-level SDMs. In the Central Tropical Indo-Pacific region, models for both levels predicted considerable range contraction in the future, but the lineage-level models predicted more severe habitat loss. Importantly, the two modelling approaches predicted opposite patterns of habitat change in the Western Tropical Indo-Pacific region. Our results highlight the necessity of conserving distinct populations and genetic pools to avoid regional extinction due to climate change and have important implications for guiding future management of seagrasses.

The Genetic Component of Seagrass Restoration: What We Know and the Way Forwards

Seagrasses are marine flowering plants providing key ecological services and functions in coasts and estuaries across the globe. Increased environmental changes fueled by human activities are affecting their existence, compromising natural habitats and ecosystems’ biodiversity and functioning. In this context, restoration of disturbed seagrass environments has become a worldwide priority to reverse ecosystem degradation and to recover ecosystem functionality and associated services. Despite the proven importance of genetic research to perform successful restoration projects, this aspect has often been overlooked in seagrass restoration. Here, we aimed to provide a comprehensive perspective of genetic aspects related to seagrass restoration. To this end, we first reviewed the importance of studying the genetic diversity and population structure of target seagrass populations; then, we discussed the pros and cons of different approaches used to restore and/or reinforce degraded populations. In general, the collection of genetic information and the development of connectivity maps are critical steps for any seagrass restoration activity. Traditionally, the selection of donor population preferred the use of local gene pools, thought to be the best adapted to current conditions. However, in the face of rapid ocean changes, alternative approaches such as the use of climate-adjusted or admixture genotypes might provide more sustainable options to secure the survival of restored meadows. Also, we discussed different transplantation strategies applied in seagrasses and emphasized the importance of long-term seagrass monitoring in restoration. The newly developed information on epigenetics as well as the application of assisted evolution strategies were also explored. Finally, a view of legal and ethical issues related to national and international restoration management is included, highlighting improvements and potential new directions to integrate with the genetic assessment. We concluded that a good restoration effort should incorporate: (1) a good understanding of the genetic structure of both donors and populations being restored; (2) the analysis of local environmental conditions and disturbances that affect the site to be restored; (3) the analysis of local adaptation constraints influencing the performances of donor populations and native plants; (4) the integration of distribution/connectivity maps with genetic information and environmental factors relative to the target seagrass populations; (5) the planning of long-term monitoring programs to assess the performance of the restored populations. The inclusion of epigenetic knowledge and the development of assisted evolution programs are strongly hoped for the future.