Wildlife population trends in protected areas predicted by national socio-economic metrics and body size.

Ensuring that protected areas (PAs) maintain the biodiversity within their boundaries is fundamental in achieving global conservation goals. Despite this objective, wildlife abundance changes in PAs are patchily documented and poorly understood. Here, we use linear mixed effect models to explore correlates of population change in 1,902 populations of birds and mammals from 447 PAs globally. On an average, we find PAs are maintaining populations of monitored birds and mammals within their boundaries. Wildlife population trends are more positive in PAs located in countries with higher development scores, and for larger-bodied species. These results suggest that active management can consistently overcome disadvantages of lower reproductive rates and more severe threats experienced by larger species of birds and mammals. The link between wildlife trends and national development shows that the social and economic conditions supporting PAs are critical for the successful maintenance of their wildlife populations

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

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/CO2 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)

Stress abiotique chez l'algue rouge Chondrus crispus (développement d'un modèle en physiologie et biologie moléculaire)

Chondrus crispus est une macroalgue rouge, choisie comme modèle d étude des Rhodophytes multicellulaires. Il est admis que la réponse de C. crispus aux agents stressants d origine abiotique relatifs à son environnement intertidal ; lumière, dessiccation, chaleur, osmolarité, pluie ; explique en grande partie sa distribution dans l estran. Le but de ma thèse est de tester cette hypothèse en utilisant des approches multi-échelles. L accent est mis notamment sur l étude du métabolisme des espèces réactives de l oxygène (ROS) considéré comme particulièrement important dans la tolérance au stress, ainsi que la photosynthèse, principal producteur de ROS et indicateur majeur de l état physiologique des végétaux. Le premier objectif était une étude génomique globale. D abord, l annotation manuelle du génome de C. crispus, afin de mieux comprendre le fonctionnement du métabolisme lié au stress et le photosynthèse. Puis, en utilisant les technologies de séquençage à haut débit, nous avons mené des expériences de transcriptomique afin de caractériser l expression des gènes des trois stades de vie majeurs de C. crispus et identifier de nouveaux candidats impliqués dans la réponse au stress, menant à de futures études plus ciblées. Le second objectif de cette thèse était d analyser la réponse de l appareil photosynthétique à la lumière, en utilisant la fluorescence de la chlorophylle et la spectrométrie, des techniques couramment utilisées chez les végétaux verts et les cyanobactéries. Cependant, les algues rouges possèdent un appareil photosynthétique unique, intermédiaire entre les plantes vertes - avecune antenne PSI similaire - et les cyanobactéries, avec des phycobilisomes en guise d antenne PSII ; les mécanismes de dissipation d énergie grâce aux caroténoïdes sont absents. Nous avons dû établir un protocole approprié afin d interpréter les données générées, et ainsi caractériser un phénomène de photoprotection original, le spill-over, un transfert d énergie efficace résultant d un contact physique entre le PSI et le PSII, contrôlé par l état redox du pool de plastoquinonesChondrus crispus is a red macroalga, chosen as a model for multicellular rhodophytes. It is believed that the response of C. crispus to abiotic stressors related to its tidal environment ; light, desiccation, heat, rainfall ; explains to a large extent its distribution on the shore. The aim of this thesis was to test this hypothesis using a multiscale approach. Two foci are the metabolism of reactive oxygen species (ROS), thought to be important in stress tolerance, and photosynthesis, the principal ROS producer and major indicator of physiological status. The first goal was a global genomic study. With the expert annotation of the C. crispus genome, for a better understanding of the functioning of the stress-related metabolism and photosynthesis. Then using next generation sequencing technologies to carry out transcriptomic experiments in order to characterize the gene expression of the three major life stages of C. crispus and identify new candidates implicated in the stress response, leading to future targeted studies. The second goal of this thesis was to analyze the response of the photosynthetic apparatus to light, using chlorophyll fluorescence and spectrometry. These technics are often used in green organisms and cyanobacteria, however, red algae possess a unique photosynthetic apparatus, intermediate between the green plants - with a similar PS I antenna - and the cyanobacteria, having phycobilisomes as PS II antenna ; they also lack known mechanisms of energy dissipation using carotenoids. We had to establish a suited protocol to interpret the generated data, and thus characterize an original and controversed photoprotection phenomenon, the spill-over, an efficient energy transfer resulting from the physical contact between PSII and PSI, controlled by the redox state of the plastoquinone poolPARIS-BIUSJ-Biologie recherche (751052107) / SudocSudocFranceF

Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae

Marine-freshwater and freshwater-marine transitions have been key events in the evolution of life, and most major groups of organisms have independently undergone such events at least once in their history. Here, we first compile an inventory of bidirectional freshwater and marine transitions in multicellular photosynthetic eukaryotes. While green and red algae have mastered multiple transitions in both directions, brown algae have colonized freshwater on a maximum of six known occasions, and angiosperms have made the transition to marine environments only two or three times. Next, we review the early evolutionary events leading to the colonization of current habitats. It is commonly assumed that the conquest of land proceeded in a sequence from marine to freshwater habitats. However, recent evidence suggests that early photosynthetic eukaryotes may have arisen in subaerial or freshwater environments and only later colonized marine environments as hypersaline oceans were diluted to the contemporary level. Although this hypothesis remains speculative, it is important to keep these alternative scenarios in mind when interpreting the current habitat distribution of plants and algae. Finally, we discuss the roles of structural and functional adaptations of the cell wall, reactive oxygen species scavengers, osmoregulation, and reproduction. These are central for acclimatization to freshwater or to marine environments. We observe that successful transitions appear to have occurred more frequently in morphologically simple forms and conclude that, in addition to physiological studies of euryhaline species, comparative studies of closely related species fully adapted to one or the other environment are necessary to better understand the adaptive processes

Marine Biotechnology

ISBN 978-90-481-8616-

NADPH oxidases in Eukaryotes: red algae provide new hints!

The red macro-alga Chondrus crispus is known to produce superoxide radicals in response to cell-free extracts of its green algal pathogenic endophyte Acrochaete operculata. So far, no enzymes involved in this metabolism have been isolated from red algae. We report here the isolation of a gene encoding a homologue of the respiratory burst oxidase gp91(phox) stop in C. crispus, named Ccrboh. This single copy gene encodes a polypeptide of 825 amino acids. Search performed in available genome and EST algal databases identified sequences showing common features of NADPH oxidases in other algae such as the red unicellular Cyanidioschyzon merolae, the economically valuable red macro-alga Porphyra yezoensis and the two diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Domain organization and phylogenetic relationships with plant, animal, fungal and algal NADPH oxidase homologues were analyzed. Transcription analysis of the C. crispus gene revealed that it was over-transcribed during infection of C. crispus gametophyte by the endophyte A. operculata, and after incubation in presence of atrazine, methyl jasmonate and hydroxyperoxides derived from C20 polyunsaturated fatty acids (PUFAs). These results also illustrate the interest of exploring the red algal lineage for gaining insight into the deep evolution of NADPH oxidases in Eukaryotes

Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers

Red algae have the most gene-rich plastid genomes known, but despite their evolutionary importance these genomes remain poorly sampled. Here we characterize three complete and one partial plastid genome from a diverse range of florideophytes. By unifying annotations across all available red algal plastid genomes we show they all share a highly compact and slowly-evolving architecture and uniquely rich gene complements. Both chromosome structure and gene content have changed very little during red algal diversification, and suggest that plastid-to nucleus gene transfers have been rare. Despite their ancient character, however, the red algal plastids also contain several unprecedented features, including a group II intron in a tRNA-Met gene that encodes the first example of red algal plastid intron maturase – a feature uniquely shared among florideophytes. We also identify a rare case of a horizontally-acquired proteobacterial operon, and propose this operon may have been recruited for plastid function and potentially replaced a nucleus-encoded plastid-targeted paralogue. Plastid genome phylogenies yield a fully resolved tree and suggest that plastid DNA is a useful tool for resolving red algal relationships. Lastly, we estimate the evolutionary rates among more than 200 plastid genes, and assess their usefulness for species and subspecies taxonomy by comparison to well-established barcoding markers such as cox1 and rbcL. Overall, these data demonstrates that red algal plastid genomes are easily obtainable using high-throughput sequencing of total genomic DNA, interesting from evolutionary perspectives, and promising in resolving red algal relationships at evolutionarily-deep and species/subspecies levels

Temperature Modulates Sex-Biased Gene Expression in the Gametophytes of the Kelp Saccharina latissima

Saccharina latissima is an economically and ecologically relevant kelp species in Europe and North America. In kelps, the sexuality is expressed during the haploid life stage and the microscopic gametophytes exhibit significant sexual dimorphism. To understand the sex-dependent impact of temperature on the gametophyte stage, we analyzed for the first time, gene expression profiles of male and female gametophytes at three different temperatures (4, 12, and 20 degrees C) characteristic for the species distribution range by using RNA-sequencing. We identified several differentially expressed genes (DEGs) between sexes; while female biased genes were enriched in general metabolism and energy production, male biased genes function within cell cycle and signaling. In our study, temperature modulated sex-biased gene expression, with only a small percentage of DEGs consistently male (7%) or female-biased (12%) at the three temperatures. Female gametophytes responded stronger to higher temperatures than males, suggesting that males are more heat tolerant. Differences between S. latissima and other brown algal gender-dependent gene expression might mirror the different evolutionary and ecological contexts. Genomic information on kelp gametophyte is still scarce and thus this study adds to our knowledge on sex differences in abiotic stress responses in macroalgae at the transcriptomic level

Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Comparative analysis of Genome-Scale Metabolic Networks (GSMNs) may yield important information on the biology, evolution, and adaptation of species. However, it is impeded by the high heterogeneity of the quality and completeness of structural and functional genome annotations, which may bias the results of such comparisons. To address this issue, we developed AuCoMe-a pipeline to automatically reconstruct homogeneous GSMNs from a heterogeneous set of annotated genomes without discarding available manual annotations. We tested AuCoMe with three datasets, one bacterial, one fungal, and one algal, and demonstrated that it successfully reduces technical biases while capturing the metabolic specificities of each organism. Our results also point out shared metabolic traits and divergence points among evolutionarily distant species, such as algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life