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Whole-genome sequencing of the seagrass Zostera , representing the first marine angiosperm genome to be fully sequenced, provides insight into the evolutionary changes associated with a transition to a marine environment in this angiosperm lineage. The genome of the seagrass Zostera marina The seagrass Zostera marina , or eelgrass, is widely distributed throughout the Northern Hemisphere. It is therefore of considerable ecological importance but — as with other seagrasses — its coastal habitats are among the world's most threatened ecosystems. Jeanine Olsen and colleagues report the whole-genome sequence of Zostera . Their analyses provide insights into the evolutionary changes associated with the 'back to the sea' reverse evolutionary trajectory that has occurred in this angiosperm lineage, including the loss of the entire repertoire of stomatal genes, and the presence of sulfated cell-wall polysaccharides that are more macro-algal-like than plant-like. Seagrasses colonized the sea 1 on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet 2 . Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes 3 , genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae 4 and that is important for ion homoeostasis, nutrient uptake and O 2 /CO 2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming 5 , 6 , to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants 7 .

The increase in extreme heat events associated to global warming threatens seagrass ecosystems, likely by affecting key plant physiological processes such as photosynthesis and respiration. Understanding species’ ability to acclimate to warming is crucial to better predict their future trends. Here, we study tolerance to warming in two key Mediterranean seagrasses, Posidonia oceanica and Cymodocea nodosa. Stress responses of shallow and deep plants were followed during and after short-term heat exposure in mesocosms by coupling photo-physiological measures with analysis of expression of photosynthesis and stress-related genes. Contrasting tolerance and capacity to heat acclimation were shown by shallow and deep P. oceanica ecotypes. While shallow plants acclimated through respiratory homeostasis and activation of photo-protective mechanisms, deep ones experienced photosynthetic injury and impaired carbon balance. This suggests that P. oceanica ecotypes are thermally adapted to local conditions and that Mediterranean warming will likely diversely affect deep and shallow meadow stands. On the other hand, contrasting mechanisms of heatacclimation were adopted by the two species. P. oceanica regulates photosynthesis and respiration at the level of control plants while C. nodosa balances both processes at enhanced rates. These acclimation discrepancies are discussed in relation to inherent attributes of the two species.

The endemic Mediterranean seagrass is highly threatened by the increased frequency and intensity of heatwaves. Meadows of the species offer a unique opportunity to unravel mechanisms marine plants activate to cope transient warming, since their wide depth distribution impose divergent heat-tolerance. Understanding these mechanisms is imperative for their conservation. Shallow and deep genotypes within the same population were exposed to a simulated heatwave in mesocosms, to analyze their transcriptomic and photo-physiological responses during and after the exposure. Shallow plants, living in a more unstable thermal environment, optimized phenotype variation in response to warming. These plants showed a pre-adaptation of genes in anticipation of stress. Shallow plants also showed a stronger activation of heat-responsive genes and the exclusive activation of genes involved in epigenetic mechanisms and in molecular mechanisms that are behind their higher photosynthetic stability and respiratory acclimation. Deep plants experienced higher heat-induced damage and activated metabolic processes for obtaining extra energy from sugars and amino acids, likely to support the higher protein turnover induced by heat. In this study we identify transcriptomic mechanisms that may facilitate persistence of seagrasses to anomalous warming events and we discovered that plants from above and below the mean depth of the summer thermocline have differential resilience to heat.

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.

Seagrass meadows provide important ecosystem services and are critical for the survival of the associated invertebrate community. However, they are threatened worldwide by human-driven environmental change. Understanding the seagrasses’ potential for adaptation is critical to assess not only their ability to persist under future global change scenarios, but also to assess the persistence of the associated communities. Here we screened a wild population of Posidonia oceanica, an endemic long-lived seagrass in the Mediterranean Sea, for genes that may be target of environmental selection, using an outlier and a genome-wide transcriptome analysis. We identified loci where polymorphism or differential expression was associated with either a latitudinal or a bathymetric gradient, as well as with both gradients in an effort to identify loci associated with temperature and light. We found the candidate genes underlying growth and immunity to be divergent between populations adapted to different latitudes and/or depths, providing evidence for local adaptation. Furthermore, we found evidence of reduced gene flow among populations including adjacent populations. Reduced gene flow, combined with low sexual recombination, small effective population size, and long generation time of P. oceanica raises concerns for the long-term persistence of this species, especially in the face of rapid environmental change driven by human activities.

The global biodiversity crisis brings significant environmental and social impacts, necessitating innovative approaches to achieve the Sustainable Development Goals. This is particularly relevant for coastal peripheries that are rich in both natural and cultural capital. The Reknotting Marine Biodiversity project adopted a trans-disciplinary approach to integrate participatory science and education, involving local communities and researchers in biodiversity monitoring using environmental DNA metabarcoding along the coast of Marina di Camerota, Southern Italy. This approach compared Posidonia oceanica habitats with areas subject to anthropogenic pressures. Results show a greater diversity of pelagic fish and benthic organisms in the presence of P. oceanica, nine species that can potentially cause Harmful Algal Blooms (HABs), and eight species responsible for non-toxic algal blooms in less pristine areas. This study highlights the value of coastal habitats and the strategic value of citizen science in raising ecological awareness, proposing a replicable model for local marine observatories jointly managed by scientists and citizens.

Aim Seed dispersal plays a key role in shaping the distribution and genetic complexity of seagrass populations and affects their resilience capacity under disturbance. The endemic seagrass Posidonia oceanica is a key component of Mediterranean coastal ecosystems, but knowledge about movement ecology in this species is limited, especially regarding seed movement pathways and dispersal potential. Location Western coast of Sicily (central Mediterranean). Methods Beach‐cast fruits of the Mediterranean seagrass P. oceanica were collected from nine localities along the Western coast of Sicily, along with adult shoots from eight putative donor meadows. We determined pair‐wise genetic differentiation between established meadows and seed cohorts. Genetic assignment tests were used to infer the most likely meadow of origin of individual seeds and were complemented with forward and backward Lagrangian simulations of dispersal. Results A significant genetic differentiation was found between seed pools and the most‐likely meadow of origin. The genetic assignment confirmed that seeds from the same cohort originated from multiple meadows and emphasised the presence of long‐distance‐dispersal (LDD) events (up to hundreds of km). Genetic connectivity appeared to be greater than that predicted by oceanographic simulations, which may reflect the longer temporal scales on which gene flow is shaped, in contrast to contemporary dispersal patterns. Lagrangian simulations highlighted that fruits were physically capable of dispersing beyond the study area and that the north Tunisian coast could be a key source of propagules for the populations studied. Main Conclusions Our study represents a significant step forward in the understanding of P. oceanica movement ecology and could guide meadows' conservation and restoration actions. Our findings are significant in a broader context outside of the research area and could be the basis of similar studies in other regions, especially considering the increasing number of fruiting events recorded across the Mediterranean likely associated with ocean warming.

Seagrasses are globally declining and often their loss is due to synergies among stressors. We investigated the interactive effects of eutrophication and burial on the Mediterranean seagrass, Posidonia oceanica. A field experiment was conducted to estimate whether shoot survival depends on the interactive effects of three levels of intensity of both stressors and to identify early changes in plants (i.e., morphological, physiological and biochemical, and expression of stress-related genes) that may serve to detect signals of imminent shoot density collapse. Sediment burial and nutrient enrichment produced interactive effects on P. oceanica shoot survival, as high nutrient levels had the potential to accelerate the regression of the seagrass exposed to high burial (HB). After 11 weeks, HB in combination with either high or medium nutrient enrichment caused a shoot loss of about 60%. Changes in morphology were poor predictors of the seagrass decline. Likewise, few biochemical variables were associated with P. oceanica survival (the phenolics, ORAC and leaf d 34 S). In contrast, the expression of target genes had the highest correlation with plant survival: photosynthetic genes (ATPa, psbD and psbA) were up-regulated in response to high burial, while carbon metabolism genes (CA-chl, PGK and GADPH) were down-regulated. Therefore, dieoffs due to high sedimentation rate in eutrophic areas can only be anticipated by altered expression of stress-related genes that may warn the imminent seagrass collapse. Management of local stressors, such as nutrient pollution, may enhance seagrass resilience in the face of the intensification of extreme climate events, such as floods.

Y.V.d.P., J.L.O., T.B.H.R. and G.P. acknowledge funding from the DOE, JGI, Berkeley, California, USA, under the Community Sequencing Program 2018, project no. 504341 (Marine Angiosperm Genomes Initiative). The work (proposal no. 10.46936/10.25585/60001196) conducted by the DOE JGI (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the DOE operated under contract no. DE-AC02-05CH11231. The Community Sequencing Program award also included support for sequencing and plant bioinformatics from HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, and DNA/RNA extraction and processing from the Arizona Genomics Institute, Tucson, Arizona. Y.V.d.P. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (grant no. 833522) and from Ghent University (Methusalem funding, grant no. BOF.MET.2021.0005.01). P.N. acknowledges funding by the Deutsche Forschungsgemeinschaft (German Research Foundation)—project no. 497665889, 1606/3-1 for research on Potamogeton. M.K. acknowledges funding through the Helmholtz School for Marine Data Science, grant no. HIDSS-0005. The work of G.P., E.D., J.P. and M.R. was partially supported by the project Marine Hazard, PON03PE_00203_1 (MUR, Italian Ministry of University and Research) and by the National Biodiversity Future Centre Program, Italian Ministry of University and Research, PNRR, Missione 4 Componente 2 Investimento 1.4 (project no. CN00000033). D.-D.M., L.L.W., M.P.T. and Y.Y.S. acknowledge funding from Universiti Malaysia Terengganu (SRG Vot55317). The work of A.A.B. was performed within the Papanin Institute for Biology of Inland Waters RAS state assignment (theme no. 121051100099-5).

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.