Browsing by Author "Procaccini, G."
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- Acoustic monitoring of O2 production of a seagrass meadowPublication . Felisberto, P.; Jesus, S. M.; Zabel, F.; Santos, Rui; Silva, João; Gobert, S.; Beer, S.; Bjork, M.; Mazzuca, S.; Procaccini, G.; Runcie, J. W.; Champenois, W.; Borges, A. V.Acoustic data were acquired in October 2011 over a Posidonia oceanica meadow in the Bay of la Revellata, Calvi, Corsica. The purpose was to develop an acoustic system for monitoring the oxygen (O2) production of an entire seagrass meadow. In a shallow water area (<38m), densely covered by P. oceanica, a sound source transmitted signals in 3 different bands (400-800Hz, 1.5-3.5kHz and 6.5-8.5kHz) toward three self-recording hydrophones at a distance of 100m, over the period of one week. The data show a high correlation between the diel cycle of the acoustic signals' energy received by the hydrophones and the temporal changes in water column O2 concentration as measured by optodes. The results thus show that a simple acoustic acquisition system can be used to monitor the O2-based productivity of a seagrass meadow at the ecosystem level with high temporal resolution. The finding of a significant production of O2 as bubbles in seagrass ecosystems suggests that net primary production is underestimated by methods that rely on the mass balance of dissolved O2 measurements. © 2015 Elsevier B.V.
- Assessing genetic diversity in clonal organisms: low diversity or low resolution? Combining power and cost efficiency in selecting markersPublication . ARNAUD-HAOND, Sophie; Alberto, F.; Teixeira, Sara; Procaccini, G.; Serrão, Ester; Duarte, C. M.The increasing use of molecular tools to study populations of clonal organisms leads us to question whether the low polymorphism found in many studies reflects limited genetic diversity in populations or the limitations of the markers used. Here we used microsatellite datasets for two sea grass species to provide a combinatory statistic, combined with a likelihood approach to estimate the probability of identical multilocus genotypes (MLGs) to be shared by distinct individuals, in order to ascertain the efficiency of the markers used and to optimize cost-efficiently the choice of markers to use for deriving unbiased estimates of genetic diversity. These results strongly indicate that conclusions from studies on clonal organisms derived using markers showing low polymorphism, including microsatellites, should be reassessed using appropriate polymorphic markers.
- Characterization of microsatellite loci in the dwarf eelgrass Zostera noltii (Zosteraceae) and cross-reactivity with Z. japonicaPublication . Coyer, J. A.; Reusch, T. B. H.; Stam, W. T.; Serrão, Ester; Pearson, G. A.; Procaccini, G.; Olsen, J. L.Zostera noltii is an important species of eelgrass occurring along European, north African, Mediterranean, Black Sea and Azov Sea coasts. Nine microsatellite loci were developed and no linkage disequilibrium was observed. Cross-amplification was observed for all loci (polymorphic) in Z. japonica ; only four loci amplified (monomorphic) in Z. marina.
- Establishing research strategies, methodologies and technologies to link genomics and proteomics to seagrass productivity, community metabolism and ecosystem carbon fluxesPublication . Mazzuca, S.; Bjork, M.; Beer, S.; Felisberto, P.; Gobert, S.; Procaccini, G.; Runcie, J. W.; Silva, João; Borges, A. V.; Brunet, C.; Buapet, P.; Champenois, W.; Costa, M. M.; D'Esposito, D.; Gullström, M.; Lejeune, P.; Lepoint, G.; Olivé, Irene; Rasmusson, L. M.; Richir, J.; Ruocco, M.; Serra, I. A.; Spadafora, A.; Santos, RuiA complete understanding of the mechanistic basis of marine ecosystem functioning is only possible through integrative and interdisciplinary research.This enables the predictionof change and possibly the mitigation of the consequences ofanthropogenic impacts. One major aim of the European Cooperation in Science and Technology (COST) Action ES0609 “Seagrasses productivity. From genes to ecosystem management,” is the calibration and synthesis of various methods and the development of innovative techniques and protocolsfor studying seagrass ecosystems. During 10 days, 20 researchers representing a range of disciplines (molecular biology, physiology, botany, ecology, oceanography, and underwater acoustics) gathered at The Station de Recherches Sous-marines et Océanographiques (STARESO, Corsica) to study together the nearby Posidonia oceanica meadow. STARESO is located in an oligotrophic area classified as “pristine site” where environmental disturbances caused by anthropogenic pressure are exceptionally low. The healthy P. oceanica meadow, which grows in front of the research station, colonizes the sea bottom from the surface to 37m depth. During the study, genomic and proteomic approaches were integrated with ecophysiological and physical approaches with the aim of understanding changes in seagrass productivity and metabolism at different depths and along daily cycles. In this paper we report details on the approaches utilized and we forecast the potential of the data that will come from this synergistic approach not only for P. oceanica but for seagrasses in general.
- Genetic structure in the Mediterranean seagrass Posidonia oceanica: disentangling past vicariance events from contemporary patterns of gene flowPublication . Serra, I. A.; Innocenti, A. M.; Di Maida, G.; Calvo, S.; Migliaccio, M.; Zambianchi, E.; Pizzigalli, C.; ARNAUD-HAOND, Sophie; Duarte, C. M.; Serrão, Ester; Procaccini, G.The Mediterranean Sea is a two-basin system, with the boundary zone restricted to the Strait of Sicily and the narrow Strait of Messina. Two main population groups are recognized in the Mediterranean endemic seagrass Posidonia oceanica, corresponding to the Western and the Eastern basins. To address the nature of the East–West cleavage in P. oceanica, the main aims of this study were: (i) to define the genetic structure within the potential contact zone (i.e. the Strait of Sicily) and clarify the extent of gene flow between the two population groups, and (ii) to investigate the role of present water circulation patterns vs. past evolutionary events on the observed genetic pattern. To achieve these goals, we utilized SSR markers and we simulated, with respect to current regime, the possible present-day dispersal pattern of Posidonia floating fruits using 28-day numerical Lagrangian trajectories. The results obtained confirm the presence of the two main population groups, without any indices of reproductive isolation, with the break zone located at the level of the Southern tip of Calabria. The populations in the Strait of Sicily showed higher affinity with Western than with Eastern populations. This pattern of genetic structure probably reflects historical avenues of recolonization from relict glacial areas and past vicariance events, but seems to persist as a result of the low connectivity among populations via marine currents, as suggested by our dispersal simulation analysis.
- Genomic DNA isolation from green and brown algae (Caulerpales and Fucales) for microsatellite library constructionPublication . E, Varela-Álvarez; Andreakis, N.; Lago-Lestón, Asunción; Pearson, G. A.; Serrão, Ester; Procaccini, G.; Duarte, C. M.; Marbà, N.A method for isolating high-quality DNA is presented for the green algae Caulerpa sp. (C. racemosa, C. prolifera, and C. taxifolia) and the brown alga Sargassum muticum. These are introduced, and invasive species in Europe, except for the native C. prolifera. Previous methods of extraction, using cetyl trimethyl ammonium bromide or various commercial kits, were used to isolate genomic DNA but either no DNA or DNA of very low quality was obtained. Genomic libraries were attempted with Caulerpa sp. on three occasions and either the restriction enzyme, the Taq polymerase, or the T4 ligase was inhibited, probably by the large amount of polysaccharides in these algae. The method presented here consists of the rapid isolation of stable nuclei, followed by DNA extraction. Yields of 6–10 μg genomic DNA from 1 g fresh blades were obtained. After genomic DNA was isolated from fresh material, the quality was checked by agarose gel. Quantification of DNA concentration was performed using UV spectrophotometric measurement of the A260/A280 ratio. The DNA was suitable for PCR, cloning, and hybridization. The DNA isolated using this method allowed successful construction of microsatellite libraries for Caulerpa species and S. muticum. The technique is inexpensive and appropriate for the isolation of multiple samples of DNA from a small amount of fresh material.
- North Atlantic phylogeography and large-scale population differentiation of the seagrass Zostera marina L.Publication . Olsen, J. L.; Stam, W. T.; Coyer, J. A.; Reusch, T. B. H.; Billingham, M. R.; Boström, C.; Calvert, E.; Christie, H.; Granger, S.; La Lumière, R.; Milchakova, N.; Oudot-Le Secq, M.- P.; Procaccini, G.; Sanjabi, B.; Serrão, Ester; Veldsink, J.; Widdicombe, S.; Wyllie-Echeverria, S.As the most widespread seagrass in temperate waters of the Northern Hemisphere, Zostera marina provides a unique opportunity to investigate the extent to which the historical legacy of the last glacial maximum (LGM18 000–10 000 years BP) is detectable in modern population genetic structure. We used sequences from the nuclear rDNA–internal transcribed spacer (ITS) and chloroplast mat K-intron, and nine microsatellite loci to survey 49 populations (> 2000 individuals) from throughout the species’ range. Minimal sequence variation between Pacific and Atlantic populations combined with biogeographical groupings derived from the microsatellite data, suggest that the trans-Arctic connection is currently open. The east Pacific and west Atlantic are more connected than either is to the east Atlantic. Allelic richness was almost two-fold higher in the Pacific. Populations from putative Atlantic refugia now represent the southern edges of the distribution and are not genetically diverse. Unexpectedly, the highest allelic diversity was observed in the North Sea–Wadden Sea–southwest Baltic region. Except for the Mediterranean and Black Seas, significant isolation-by-distance was found from ~150 to 5000 km. A transition from weak to strong isolation-by-distance occurred at ~150 km among northern European populations suggesting this scale as the natural limit for dispersal within the metapopulation. Links between historical and contemporary processes are discussed in terms of the projected effects of climate change on coastal marine plants. The identification of a high genetic diversity hotspot in Northern Europe provides a basis for restoration decisions.
- Population genetics of dwarf eelgrass Zostera nolti throughout its biogeographic rangePublication . Coyer, J. A.; Diekmann, Onno; Serrao, Ester; Procaccini, G.; Milchakova, N.; Pearson, Gareth; Stam, W. T.; Olsen, J. L.The marine angiosperm Zostera noltii (dwarf eelgrass), an important facilitator species and food source for invertebrates and waterfowl, predominantly inhabits intertidal habitats along eastern Atlantic shores from Mauritania to southern Norway/Kattegat Sea and throughout the Mediterranean, Black and Azov seas. We used 9 microsatellite loci to characterize population structure at a variety of spatial scales among 33 populations from 11 localities throughout the entire biogeographic range. Isolation by distance analysis suggested a panmictic genetic neighborhood of 100 to 150 km. At the global scale, a neighbor-joining tree based on Reynolds distances revealed strongly-supported groups corresponding to northern Europe, Mauritania and the Black/Azov Sea; separate Mediterranean and Atlantic-Iberian groups were poorly supported. Clones (genets with multiple ramets) were present in most populations but were generally small (ca. < 3 m(2)). Exceptions were found in Mauritania (ca. 29 m in length), the Azov Sea (ca. 40 m in length) and the Black Sea (ca. 50 m in length). Although genetic diversity and allelic richness generally decreased from Mauritania to Denmark, the putative post-glacial recolonization route, both were unexpectedly high among populations from the German Wadden Sea.
- Population genetics of dwarf eelgrass Zostera noltii throughout its biogeographic rangePublication . Coyer, J. A.; Diekmann, O. E.; Serrão, Ester; Procaccini, G.; Milchakova, N.; Pearson, G. A.; Stam, W. T.; Olsen, J. L.The marine angiosperm Zostera noltii (dwarf eelgrass), an important facilitator species and food source for invertebrates and waterfowl, predominantly inhabits intertidal habitats along eastern Atlantic shores from Mauritania to southern Norway/Kattegat Sea and throughout the Mediterranean, Black and Azov seas. We used 9 microsatellite loci to characterize population structure at a variety of spatial scales among 33 populations from 11 localities throughout the entire biogeographic range. Isolation by distance analysis suggested a panmictic genetic neighborhood of 100 to 150 km. At the global scale, a neighbor-joining tree based on Reynolds distances revealed strongly-supported groups corresponding to northern Europe, Mauritania and the Black/Azov Sea; separate Mediterranean and Atlantic-Iberian groups were poorly supported. Clones (genets with multiple ramets) were present in most populations but were generally small (ca. <3 m2). Exceptions were found in Mauritania (ca. 29 m in length), the Azov Sea (ca. 40 m in length) and the Black Sea (ca. 50 m in length). Although genetic diversity and allelic richness generally decreased from Mauritania to Denmark, the putative post-glacial recolonization route, both were unexpectedly high among populations from the German Wadden Sea.
- Response of key stress-related genes of the seagrass Posidonia oceanica in the vicinity of submarine volcanic ventsPublication . Lauritano, C.; Ruocco, M.; Dattolo, E.; Buia, M. C.; Silva, João; Santos, Rui; Olivé, Irene; Costa, M. M.; Procaccini, G.Submarine volcanic vents are being used as natural laboratories to assess the effects of increased ocean acidity and carbon dioxide (CO2) concentration on marine organisms and communities. However, in the vicinity of volcanic vents other factors in addition to CO2, which is the main gaseous component of the emissions, may directly or indirectly confound the biota responses to high CO2. Here we used for the first time the expression of antioxidant and stress-related genes of the seagrass Posidonia oceanica to assess the stress levels of the species. Our hypothesis is that unknown factors are causing metabolic stress that may confound the putative effects attributed to CO2 enrichment only. We analyzed the expression of 35 antioxidant and stress-related genes of P. oceanica in the vicinity of submerged volcanic vents located in the islands of Ischia and Panarea, Italy, and compared them with those from control sites away from the influence of vents. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) was used to characterize gene expression patterns. Fifty-one percent of genes analyzed showed significant expression changes. Metal detoxification genes were mostly down-regulated in relation to controls at both Ischia and Panarea, indicating that P. oceanica does not increase the synthesis of heavy metal detoxification proteins in response to the environmental conditions present at the two vents. The up-regulation of genes involved in the free radical detoxification response (e.g., CAPX, SODCP and GR) indicates that, in contrast with Ischia, P. oceanica at the Panarea site faces stressors that result in the production of reactive oxygen species, triggering antioxidant responses. In addition, heat shock proteins were also activated at Panarea and not at Ischia. These proteins are activated to adjust stress-accumulated misfolded proteins and prevent their aggregation as a response to some stressors, not necessarily high temperature. This is the first study analyzing the expression of target genes in marine plants living near natural CO2 vents. Our results call for contention to the general claim of seagrasses as "winners" in a high-CO2 world, based on observations near volcanic vents. Careful consideration of factors that are at play in natural vents sites other than CO2 and acidification is required. This study also constitutes a first step for using stress-related genes as indicators of environmental pressures in a changing ocean.