A king and vassals' tale: Molecular signatures of clonal integration in Posidonia oceanica under chronic light shortage

Under unfavourable conditions, clonal plants benefit from physiological integration among ramets, sharing resources and information. Clonal integration can buffer against environmental changes and lets the plant clone work as a ‘macro’ organism. Molecular signals that regulate this phenomenon are completely unknown in marine plants. Here we present a first comprehensive study providing insights into the metabolic role of different types of ramets (i.e. apical vs. vertical) in the foundation species Posidonia oceanica. Plants were exposed to 80% diminishing irradiance level (LL) in a controlled mesocosm system. Subsequent multiscale variations in whole transcriptome expression, global DNA methylation level, photo-physiology, morphology and fitness-related traits, were explored at different exposure times. We tested the hypothesis that vertical shoots (the ‘vassals’) can provide vital resources to apical shoots (the ‘kings’) under energy shortage, thus safeguarding the whole clone survival. Whole transcriptome analysis of leaves and shoot-apical meristems (SAMs) emphasized signatures of molecular integration among ramets, which strongly correlated with higher organization-level responses. In both shoots types, the exposure to LL resulted in a growth slowdown throughout the experiment, which started from immediate signals in SAMs. In apical shoots, this was linked to an acclimative response, where they were suffering a mild stress condition, while in vertical ones it fell in a more severe stress response. Yet, they suffered from sugar starvation and showed a clear cellular stress response in terms of protein refolding and DNA repair mechanisms. Several epigenetic mechanisms modulated the observed gene-expression patterns and the cross-talk between DNA methylation and the cellular energetic status appeared to regulate shoot metabolism under LL. Synthesis. Our results demonstrate a high level of specialization of integrated ramets within seagrass clones and a ‘division of labour’ under adverse conditions. Vertical shoots appear to do ‘most of the job’ especially in terms of resource providing, whereas activated functions in apical shoots were restricted to few important processes, according to an ‘energy-saving’ strategy. The response of vertical shoots could be seen as a ‘sacrificing response’ allowing the survival of ‘the king’ that is key for ensuring propagation and population maintenance, and for the colonization of new environments

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

Does Warming Enhance the Effects of Eutrophication in the Seagrass Posidonia oceanica?

Seagrass meadows are disappearing at rates comparable to those reported for mangroves, coral reefs, and tropical rainforests. One of the main causes of their decline is the so-called cultural eutrophication, i.e., the input of abnormal amounts of nutrients derived from human activities. Besides the impact of eutrophication at a local scale, the occurrence of additional stress factors such as global sea warming may create synergisms in detriment of seagrass meadows’ health. In the present study, we aimed to evaluate if plants undergoing chronic cultural eutrophication and plants growing in relatively pristine waters are more (or less) sensitive to heat stress, nutrient load and the combination of both stressors. To address this question, a mesocosm experiment was conducted using Posidonia oceanica collected from two environments with different nutrients load history. Plants were exposed in controlled conditions to high nutrient concentrations, increased temperature and their combination for 5 weeks, to assess the effect of the single stressors and their interaction. Our results revealed that plants experiencing chronic cultural eutrophication (EU) are more sensitive to further exposure to multiple stressors than plants growing in oligotrophic habitats (OL). OL and EU plants showed different morphological traits and physiological performances, which corroborates the role of local pressures in activating different strategies in response to global environmental changes. EU-plants appeared to be weaker during the treatments, showing the greatest percentage of mortality, particularly under increased temperature. Temperature and nutrient treatments showed opposite effects when tested individually and an offset response when combined. The activation of physiological strategies with high energetic expenses to cope with excess of nutrients and other stressors, could affect plants present and future persistence, particularly under eutrophic conditions. Our results represent a step forward in understanding the complex interactions that occur in natural environments. Moreover, unraveling intraspecific strategies and the role of local acclimation/adaptation in response to multiple stressors could be crucial for seagrass conservation strategies under a climate change scenario

Effects of Current and Future Summer Marine Heat Waves on Posidonia oceanica: Plant Origin Matters?

Marine heat waves (MHWs), prolonged discrete anomalously warm water events, have been increasing significantly in duration, intensity and frequency all over the world, and have been associated with a variety of impacts including alteration of ecosystem structure and function. This study assessed the effects of current and futureMHWs on the Mediterranean seagrass Posidonia oceanica performance, also testing the importance of the thermal environment where the plant lives. The effects of current MHWs were studied through a mensurative experiment in a cold and in a warm site (West and North-West Sardinia, Italy, respectively). Future MHWs effects were tested through a manipulative experiment using P. oceanica shoots collected fromthe cold and warmsites and transplanted in a common garden in front of a power plant (North-West Sardinia): here plants were exposed to heat longer in duration and stronger in intensity than the natural MHWs of the last 20 years, resembling the future scenario. Morphological (total # of leaves, maximum leaf length, and percentage of total necrotic leaf length per shoot) and biochemical variables (leaf proteins, carbohydrates, and lipids) were considered. Plants had similar sublethal responses in both the experiments for most of the variables, revealing that current and future MHWs had similar effect types, but different in magnitude depending on the intensity of the waves: in general, the number of leaves, the maximum leaf length and lipid content decreased, while the leaf necrosis and carbohydrates increased. However, also the origin of the plants affected the results, corroborating the hypothesis that the thermal context the plants live affects their tolerance to the heat. Overall, this study provided evidence about the importance of biochemical variations, such as carbohydrate and lipid levels, as potentially good indicators of seagrass heat stress

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

Trace Elements and Carbon and Nitrogen Stable Isotopes in Organisms from a Tropical Coastal Lagoon

Trace elements (Fe, Mn, Al, Zn, Cr, Cu, Ni, Pb, Cd, Hg, and As) and stable isotope ratios (δ13C and δ15N) were analyzed in sediments, invertebrates, and fishes from a tropical coastal lagoon influenced by iron ore mining and processing activities to assess the differences in trace element accumulation patterns among species and to investigate relations with trophic levels of the organisms involved. Overall significant negative relations between trophic level (given by 15N) and trace element concentrations in gastropods and crustaceans showed differences in internal controls of trace element accumulation among the species of different trophic positions, leading to trace element dilution. Generally, no significant relation between δ15N and trace element concentrations was observed among fish species, probably due to omnivory in a number of species as well as fast growth. Trace element accumulation was observed in the fish tissues, with higher levels of most trace elements found in liver compared with muscle and gill. Levels of Fe, Mn, Al, and Hg in invertebrates, and Fe and Cu in fish livers, were comparable with levels in organisms and tissues from other contaminated areas. Trace element levels in fish muscle were below the international safety baseline standards for human consumption

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

DATA AVAILABILITY : The DNA sequencing data for the C. nodosa genome assembly have been deposited in the NCBI database under BioProject PRJNA1041560 via the link https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1041560. All assemblies and annotations for all seagrass species discussed in the current paper can be found at https://bioinformatics.psb.ugent.be/gdb/seagrasses/. The transcriptome data (including raw data and clean data) and sequencing QC reports for C. nodosa can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Cymnodnscriptome_2, the transcriptome data and sequencing QC reports for P. oceanica can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Posocenscriptome_2, the transcriptome data and sequencing QC reports for T. testudinum can be found at https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Thatesnscriptome_4 and the transcriptome data for Z. marina are from ref. 15. For the public databases, the RFAM database v.14.7 can be downloaded at https://ftp.ebi.ac.uk/pub/databases/Rfam/14.7/, the UniProt database can be accessed from the web at http://www.uniprot.org and downloaded from http://www.uniprot.org/downloads and the NCBI nucleotide database can be accessed via https://www.ncbi.nlm.nih.gov/.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.The DOE, JGI, Berkeley, California, USA, under the Community Sequencing Program 2018; the European Research Council under the European Union’s Horizon 2020 research and innovation programme ; Ghent University (Methusalem funding); the Deutsche Forschungsgemeinschaft (German Research Foundation); the Helmholtz School for Marine Data Science; 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; and Universiti Malaysia Terengganu.https://www.nature.com/nplants2024-07-26hj2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-14:Life below wate

Review 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

Photo-physiology and morphology reveal divergent warming responses in northern and southern hemisphere seagrasses

A better understanding of species and population responses to thermal stress is critical to predict changes in their distribution under warming scenarios. Seagrasses are a unique group of marine plants that play fundamental roles in marine environments and provide vital ecosystem services. Nevertheless, previous studies on seagrass thermal tolerance have focused exclusively on a handful of species, with the majority of these remaining virtually unexplored. Moreover, to date, no study has compared the response to thermal stress between northern and southern hemisphere seagrasses. Here, we conducted comparative mesocosm experiments using four seagrass species from the northern (i.e. Mediterranean: Posidonia oceanica, Cymodocea nodosa) and southern (i.e. Australia: Posidonia australis and Zostera muelleri) hemisphere as representative of two different life strategies, i.e. climax (P. oceanica, P. australis) and pioneer (C. nodosa, Z. muelleri). Plants acclimatized to the mesocosm conditions at ambient temperature (i.e. 26 °C) during a 5-week period, were exposed to a simulated marine heatwave (i.e. 32 °C) for 2 weeks. Measurements of plant responses, including photo-physiology, morphology, and pigment content, were performed at the end of the warming exposure. Results showed that warming had no significant effects on photosynthetic performances of northern hemisphere seagrasses while negatively impacted their southern hemisphere counterparts. Similarly, warming favored the growth of northern hemisphere plants, but strongly inhibited the development of southern hemisphere species. Furthermore, photo-physiological and pigment content results suggested pioneer seagrasses better dealt with warming than climax species. Our study provides more insights into the field of seagrass ecology and yields potential implication for future seagrass conservation and restoration activities

Local environment modulates whole-transcriptome expression in the seagrass Posidonia oceanica under warming and nutrients excess

The intensification of anomalous events of seawater warming and the co-occurrence with local anthropogenic stressors are threatening coastal marine habitats, including seagrasses, which form extensive underwater meadows. Eutrophication highly affects coastal environments, potentially summing up to the widespread effects of global climate changes. In the present study, we investigated for the first time in seagrasses, the transcriptional response of different plant organs (i.e., leaf and shoot apical meristem, SAM) of the Mediterranean seagrass Posidonia oceanica growing in environments with a different history of nutrient enrichment. To this end, a mesocosm experiment exposing plants to single (nutrient enrichment or temperature increase) and multiple stressors (nutrient enrichment plus temperature increase), was performed. Results revealed a differential transcriptome regulation of plants under single and multiple stressors, showing an organ-specific sensitivity depending on plants' origin. While leaf tissues were more responsive to nutrient stress, SAM revealed a higher sensitivity to temperature treatments, especially in plants already impacted in their native environment. The exposure to stress conditions induced the modulation of different biological processes. Plants living in an oligotrophic environment were more responsive to nutrients compared to plants from a eutrophic environment. Evidences that epigenetic mechanisms were involved in the regulation of transcriptional reprogramming were also observed in both plants’ organs. These results represent a further step in the comprehension of seagrass response to abiotic stressors pointing out the importance of local pressures in a global warming scenario