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Aubert, A., Antajan, E., Lynam, C., Pitois, S., Pliru, A., Vaz, S., et al. (2018). No more reason for ignoring gelatinous zooplankton in ecosystem assessment and marine management: Concrete cost-effective methodology during routine fishery trawl surveys. Mar. Pol., 89, 100–108.
Résumé: Gelatinous zooplankton, including cnidarians, ctenophores, and tunicates (appendicularians, pyrosomes, salps and doliolids), are often overlooked by scientific studies, ecosystem assessments and at a management level. Despite the important economic consequences that they can have on human activities and on the marine food web, arguments often related to the costs of monitoring or their coordination, or simply negligence, have resulted in the absence of relevant monitoring programs. A cost-effective protocol has been applied on trawling from existing fishery surveys conducted by national laboratories in England and France. The testing phase has successfully demonstrated the adequacy of such a tool to sample macro- and mega-zooplankton gelatinous organisms in a cost-effective way. This success has led to the acceptance of this protocol into the French implementation of the EU's Marine Strategy Framework Directive (MSFD). Here, a protocol which can be applied to any trawl-based fishery survey and in any new large-scale monitoring program is provided. As an ecosystem approach to marine management is currently adopted, exemplified by the MSFD in Europe, gelatinous zoo plankton should be monitored correctly to prevent a knowledge gap and bias to ecosystem assessments in future.
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Auguet, J. C., Montanie, H., & Lebaron, P. (2006). Structure of virioplankton in the Charente Estuary (France): transmission electron microscopy versus pulsed field gel electrophoresis. Microb Ecol, 51(2), 197–208.
Résumé: Changes in the composition of viral communities were investigated along a salinity gradient and at different times by means of transmission electron microscopy (TEM) and pulsed field gel electrophoresis (PFGE). Samples were collected in fresh (Charente River), estuarine (Charente Estuary), and coastal (Pertuis d'Antioche, French Atlantic coast) waters. Both methods revealed similar patterns in viral community structure with a dominance of small viral particles (capsid and genome size). Viruses with a head size below 65 nm made up 71 +/- 5% of total virus-like particles, and virus-like genomes (VLG) below 100 kb accounted for 89 +/- 9% of total VLG. Despite this apparent stability of virioplankton composition over spatial scale (salinity gradient), the occurrence of large viruses (capsid and genome size) in estuarine and seawater samples indicated the presence of viral populations specific to a geographical location. Temporal changes in the structure (capsid and genome size) of viral communities were more pronounced than those reported at the spatial scale. From January to May 2003, seasonal changes in viral abundance and bacterial production occurred concomitantly with an increase in viral genomic diversity (richness), suggesting that virioplankton composition was strongly linked to changes in microbial activity and/or in the structure of the host communities. Although PFGE and TEM yielded complementary results in the description of virioplankton structures, it seems that the use of PFGE alone should be enough for the monitoring of community changes.
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Baudrier, J., Lefebvre, A., Galgani, F., Saraux, C., & Doray, M. (2018). Optimising French fisheries surveys for marine strategy framework directive integrated ecosystem monitoring. Marine Policy, 94, 10–19.
Résumé: The French initial assessment of the Marine Strategy Framework Directive (MSFD) highlighted the lack of reliable data concerning offshore areas. During the planning of the monitoring programmes, the scientists therefore proposed to partially cover this gap by using existing fisheries research vessel surveys deployed for the purposes of the Common Fisheries Policy (CFP). This paper describes ways of improving the effectiveness of these surveys and making them better suited to delivering the information needed for the MSFD. The process took two years and became operational at the beginning of the year 2016. Testing phases from October 2013 to August 2015 had to be organized to fit within the ongoing fisheries tasks without significantly increasing the workload in terms of both time and human resources. Six fisheries research surveys henceforth collect new data, with or without additional sampling techniques. Specific examples are given with litter and hydrological data which will be used to assess the environmental status of French marine waters. The paper also identifies certain limitations regarding this approach. This French experiment enabled more efficient and effective use of current data collection efforts, while optimising vessel time and implementing an ecosystem approach in collecting data for fisheries management.
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Brandt, M., Trouche, B., Henry, N., Liautard-Haag, C., Maignien, L., de Vargas, C., et al. (2020). An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities. Front. Mar. Sci., 7, 234.
Résumé: The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from similar to 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (>= 10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNA for logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (>= 10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.
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Brosset, P., Fromentin, J. - M., Van Beveren, E., Lloret, J., Marques, V., Basilone, G., et al. (2017). Spatio-temporal patterns and environmental controls of small pelagic fish body condition from contrasted Mediterranean areas. Progress in Oceanography, 151, 149–162.
Résumé: Small pelagic fish are among the most ecologically and economically important marine fish species and are characterized by large fluctuations all over the world. In the Mediterranean Sea, low catches and biomass of anchovies and sardines have been described in some areas during the last decade, resulting in important fisheries crises. Therefore, we studied anchovy and sardine body condition variability, a key index of population health and its response to environmental and anthropogenic changes. Wide temporal and spatial patterns were investigated by analyzing separately data from scientific surveys and fisheries in eight Mediterranean areas between 1975 and 2015.
Results showed that anchovy and sardine body condition as well as maximum size in some areas sharply decreased in most Mediterranean areas along years (except in the Northern Alboran Sea). Despite this general pattern, well-marked environmental differences between sub-regions were highlighted by several analyses and variations in body condition were not found to be homogeneous over all the Mediterranean Sea. Further, other analyses revealed that except for the Adriatic where major changes towards a lower body condition were concomitant with a decrease in river runoffs and chl-a concentration, no concomitant environmental regime shift was detected in other areas. Together, these analyses highlighted the current poor body condition of almost all small pelagic fish populations in the Mediterranean. Yet, global environmental indices could not explain the observed changes and the general decrease in condition might more likely come from regional environmental and/or anthropogenic (fishing) effects. A prolonged state of poor fish body condition, together with an observed reduced size and early age-at-maturity may have strong ecological, economic and social consequences all around the Mediterranean Sea. Mots-Clés: Anchovy; Fish health; Marine monitoring; Sardine
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