Unravelling the Complexity of the Molecular and Physiological Response to Environmental Change in Seagrasses

This thesis explores the complexity of seagrass stress response in the face of current environmental changes. This is a timely and relevant issue due to the role supplied by these foundation species in coastal ecosystems, and the dramatic consequences their loss would cause on marine biodiversity and human well-being. Using as target species the iconic Mediterranean seagrass Posidonia oceanica, here I show: i) how molecular reprogramming, acting primarily at gene-expression level, coordinates physiological and morphological responses to different stressors, and ultimately determines species’ acclimation strategies and tolerance capacity; ii) the differential stress response existing within and among different organs, and between different shoot types; iii) how the response to a single stressor can be modified depending on its temporal variability, and due to the interaction with another stressor. In this study, new transcriptome data have been generated, from leaves and shoot-apical meristems, increasing considerably molecular resources available for future studies on seagrass evolutionary ecology and functional genomics. Moreover, this research sheds first light on the stress response of organs other than leaf, in seagrasses, and recognises the shoot meristem as a key determinant of whole plant survival. Common and stress-specific molecular biomarkers have been identified through different approaches, and their potential applicability as sub-lethal stress indicators can be verified in the future with ad hoc experiments. Another important aspect of this study is the recognition of the importance of epigenetic variations, specifically DNA methylation changes, as key mechanisms for phenotypic accommodation and adaptive responses to environmental changes in seagrasses. Tolerance capacity of the species to main current threats of coastal areas, namely the reduction of available light, heat stress, eutrophication and herbivory, is discussed in light of the results obtained from the different experiments

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.info:eu-repo/semantics/publishedVersio

Linking gene expression to productivity to unravel long-and short-term responses of seagrasses exposed to CO2 in volcanic vents

Ocean acidification is a major threat for marine life but seagrasses are expected to benefit from high CO2. In situ (long-term) and transplanted (short-term) plant incubations of the seagrass Cymodocea nodosa were performed near and away the influence of volcanic CO2 vents at Vulcano Island to test the hypothesis of beneficial effects of CO2 on plant productivity. We relate, for the first time, the expression of photosynthetic, antioxidant and metal detoxification-related genes to net plant productivity (NPP). Results revealed a consistent pattern between gene expression and productivity indicating water origin as the main source of variability. However, the hypothesised beneficial effect of high CO2 around vents was not supported. We observed a consistent long-and short-term pattern of gene downregulation and 2.5-fold NPP decrease in plants incubated in water from the vents and a generalized upregulation and NPP increase in plants from the vent site incubated with water from the Reference site. Contrastingly, NPP of specimens experimentally exposed to a CO2 range significantly correlated with CO2 availability. The down-regulation of metal-related genes in C. nodosa leaves exposed to water from the venting site suggests that other factors than heavy metals, may be at play at Vulcano confounding the CO2 effects.ESF COST Action [ES0906]; Portuguese Foundation for Science and Technology (FCT) [PTDC/MAR-EST/3687/2012]; Italian MIUR Flagship project RITMARE (NRP); FCT [UID/Multi/04326/2013, SFRH/BPD/71129/2010, SFRH/BD/64590/2009]info:eu-repo/semantics/publishedVersio

m6A RNA Methylation in marine plants: first insights and relevance for biological rhythms

Circadian regulations are essential for enabling organisms to synchronize physiology with environmental light-dark cycles. Post-transcriptional RNA modifications still represent an understudied level of gene expression regulation in plants, although they could play crucial roles in environmental adaptation. N6-methyl-adenosine (m6A) is the most prevalent mRNA modification, established by "writer" and "eraser" proteins. It influences the clockwork in several taxa, but only few studies have been conducted in plants and none in marine plants. Here, we provided a first inventory of m6A-related genes in seagrasses and investigated daily changes in the global RNA methylation and transcript levels of writers and erasers in Cymodocea nodosa and Zostera marina. Both species showed methylation peaks during the dark period under the same photoperiod, despite exhibiting asynchronous changes in the m6A profile and related gene expression during a 24-h cycle. At contrasting latitudes, Z. marina populations displayed overlapping daily patterns of the m6A level and related gene expression. The observed rhythms are characteristic for each species and similar in populations of the same species with different photoperiods, suggesting the existence of an endogenous circadian control. Globally, our results indicate that m6A RNA methylation could widely contribute to circadian regulation in seagrasses, potentially affecting the photo-biological behaviour of these plants.FCT: UIDB/04326/2020info:eu-repo/semantics/publishedVersio

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

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

Here, we report the first use of massive-scale RNA-sequencing to explore seagrass response to CO2-driven ocean acidification (OA). Large-scale gene expression changes in the seagrass Cymodocea nodosa occurred at CO2 levels projected by the end of the century. C. nodosa transcriptome was obtained using Illumina RNA-Seq technology and de novo assembly, and differential gene expression was explored in plants exposed to short-term high CO2/low pH conditions. At high pCO(2), there was a significant increased expression of transcripts associated with photosynthesis, including light reaction functions and CO2 fixation, and also to respiratory pathways, specifically for enzymes involved in glycolysis, in the tricarboxylic acid cycle and in the energy metabolism of the mitochondrial electron transport. The upregulation of respiratory metabolism is probably supported by the increased availability of photo-synthates and increased energy demand for biosynthesis and stress-related processes under elevated CO2 and low pH. The upregulation of several chaperones resembling heat stress-induced changes in gene expression highlighted the positive role these proteins play in tolerance to intracellular acid stress in seagrasses. OA further modifies C. nodosa secondary metabolism inducing the transcription of enzymes related to biosynthesis of carbon-based secondary compounds, in particular the synthesis of polyphenols and isoprenoid compounds that have a variety of biological functions including plant defence. By demonstrating which physiological processes are most sensitive to OA, this research provides a major advance in the understanding of seagrass metabolism in the context of altered seawater chemistry from global climate change.Portuguese FCT project HighGrass [PTDC/MAR-EST/3687/2012

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

A pan-European epidemiological study reveals honey bee colony survival depends on beekeeper education and disease control

Reports of honey bee population decline has spurred many national efforts to understand the extent of the problem and to identify causative or associated factors. However, our collective understanding of the factors has been hampered by a lack of joined up trans-national effort. Moreover, the impacts of beekeeper knowledge and beekeeping management practices have often been overlooked, despite honey bees being a managed pollinator. Here, we established a standardised active monitoring network for 5 798 apiaries over two consecutive years to quantify honey bee colony mortality across 17 European countries. Our data demonstrate that overwinter losses ranged between 2% and 32%, and that high summer losses were likely to follow high winter losses. Multivariate Poisson regression models revealed that hobbyist beekeepers with small apiaries and little experience in beekeeping had double the winter mortality rate when compared to professional beekeepers. Furthermore, honey bees kept by professional beekeepers never showed signs of disease, unlike apiaries from hobbyist beekeepers that had symptoms of bacterial infection and heavy Varroa infestation. Our data highlight beekeeper background and apicultural practices as major drivers of honey bee colony losses. The benefits of conducting trans-national monitoring schemes and improving beekeeper training are discussed

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

Frontiers in Marine Science - Marine Molecular Biology and Ecology

Biologia ed Ecologia Marin