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Janssen A.,Senckenberg Institute | Chevaldonne P.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Arbizu P.M.,Senckenberg Institute
Marine Ecology Progress Series | Year: 2013

The 3PP marine cave near Marseille (NW Mediterranean) is at a depth of only 15 m. Nevertheless, the cave is a unique deep-sea-like habitat zone due to total darkness, lack of water circulation, oligotrophy, and cold homothermy, a thermal regime similar to that of the deep Mediterranean. We studied the meiofaunal community composition and diversity at 3 sampling stations in the cave (entrance, middle, and blind end). Major taxon composition, based on presence/ absence data, did not vary over the transect; however, significant differences in community were found. Tardigrades were the only major taxon restricted to the inner parts of the cave. Copepod diversity decreased towards the inner parts of the cave. The 3PP Cave was characterized by very low abundances of meiofaunal organisms similar to abyssal sites elsewhere. A total of 405 individual copepods were assigned to 27 families and 90 species (75% of them new to science). Significant differences in copepod communities between stations were found at family, genus, and species level. Some harpacticoid taxa generally known from the deep sea, such as Marsteinia, Ancorabolina, Paranannopus, Nematovorax, and Argestidae, were represented in the 3PP Cave. A naive Bayes model was used for the first time to classify the communities as 'shallow' or 'abyssal'. The meiobenthic communities at the entrance and the end of the cave were unequi - vocally classified as 'shallow' and 'abyssal' respectively, while the middle part of the cave presented a mixed community. Our study further highlights the strong faunal and community affinities between marine caves and the deep sea, indicating the existence of dispersal mechanisms from deep waters into the euphotic zone for benthic organisms. © Inter-Research 2013.


Robin V.,University of Kiel | Nelle O.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental
Vegetation History and Archaeobotany | Year: 2014

Fire caused by humans played an important role in prehistoric clearance of woodland, which was a prerequisite for the rise of agriculture since at least the Neolithic revolution. Therefore, reconstructed fire history provides insights into the spread of agriculture. However, for central Europe, the past fire regime is still poorly known. Thus, to help to fill this gap, fire history has been investigated using data relevant at a local scale, which is the scale of woodland clearance processes according to local human practices. For this purpose, soil/soil sediment charcoal analysis has been conducted at four sites in northern Germany and five in central Germany. At each site, four to nine sequences of soil/soil sediment were excavated, described in the field and sampled. The sampled material has been differentiated by soil horizons formed in situ and colluvial sediments. The charcoal content of both types of sampled material was quantified and some of it was taxonomically analysed. Chronological information was obtained by radiocarbon dating 73 single charcoal pieces that had previously been identified taxonomically. Such data sets have permitted us to identify a minimum number of fire events for every site, which had burnt various types of woodlands and at different chronological phases. Based on the local scale data, regional trends were identified. Charcoals from the late Pleistocene and early Holocene derived from conifers only, and these most probably indicate wildfire events in flammable woodlands. Charcoals dated to the mid and late Holocene derived predominantly from broad-leaved trees probably resulting from human-ignited fires in weakly flammable woodlands. The calculated minimum fire frequency indicates an increase in fire occurrences during the Holocene following the phases of cultural human development. This supports the importance of human-made fire in northern central Europe during the Holocene. Such minimum fire frequency appears much higher during the iron age and the middle ages, but not before. This fits with the general statement of regional woodland loss and landscape opening relatively recently, during the late Holocene. © 2014 Springer-Verlag Berlin Heidelberg.


Coiffait-Gombault C.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Buisson E.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Dutoit T.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental
Applied Vegetation Science | Year: 2012

Questions: Is it possible to restore a target herbaceous plant community on ex-arable land by sowing foundation species? What is the impact of sheep grazing on the restoration of this ecosystem? How can we rapidly evaluate the success of restoration methods? Location: Nature reserve of the plain of La Crau, southeast France (43° 31' N, 4° 50' E) Methods: In an ex-arable field, we sowed an indigenous species mix in 2007. This was composed of two perennial species dominant in the reference grassland ecosystem (Brachypodium retusum, Thymus vulgaris) and one annual species (Trifolium subterraneum) also found on the reference grassland and which is well-known for its ability to quickly cover bare soil. These three species are called foundation species as they play an essential role in structuring the restored ecosystem community. To investigate the significances of the foundation species on community dynamics, four subordinate species were sown 1 yr later: Taeniatherum caput-medusae, Linum strictum, Evax pygmaea and Asphodelus ayardii. The subordinate species are typical plants of the reference grassland which describe well this vegetation type. Results: Sowing foundation species was an effective means of reintroducing them. Their presence in the ex-arable field very rapidly promoted establishment of grassland species and impeded establishment of weeds. When grazing was excluded, the foundation species covered the ground, particularly with Trifolium subterraneum, which reached 54% ground cover. Subordinate species established better on the foundation species sown treatment and on the grazed treatment. Conclusion: In the short term, sowing indigenous foundation species and maintaining grazing seems to be a good method to restore grassland plant communities that have a poor ability to re-establish spontaneously. This study also demonstrates that sowing and monitoring of subordinate species is an effective method to rapidly test whether a particular restoration protocol will have a positive effect on community assembly and development. © 2012 International Association for Vegetation Science.


Bendahmane M.,CNRS Laboratory of Plant Reproduction and Development | Dubois A.,CNRS Laboratory of Plant Reproduction and Development | Raymond O.,CNRS Laboratory of Plant Reproduction and Development | Bris M.L.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental
Journal of Experimental Botany | Year: 2013

Roses hold high symbolic value and great cultural importance in different societies throughout human history. They are widely used as garden ornamental plants, as cut flowers, and for the production of essential oils for the perfume and cosmetic industries. Domestication of roses has a long and complex history, and the rose species have been hybridized across vast geographic areas such as Europe, Asia, and the Middle East. The domestication processes selected several flower characters affecting floral quality, such as recurrent flowering, double flowers, petal colours, and fragrance. The molecular and genetic events that determine some of these flower characters cannot be studied using model species such as Arabidopsis thaliana, or at least only in a limited manner. In this review, we comment on the recent development of genetic, genomic, and transcriptomic tools for roses, and then focus on recent advances that have helped unravel the molecular mechanisms underlying several rose floral traits. © 2013 The Author.


Azemard C.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Vieillescazes C.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Menager M.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental
Microchemical Journal | Year: 2014

In this study, natural varnishes used in ancient painting techniques were recreated following ancient recipes. They were irradiated by artificial sunlight and analysed by FT-IR all along the accelerated ageing. The main natural resins used were: sandarac, copal, colophony, mastic and dammar in alcohol, spirit turpentine and oil media. This study aims to understand and follow the evolution of characteristic absorption bands for the differentiation of varnish types by FT-IR analyses. Kinetics and evolutions of the compositions of the varnishes during photo-ageing were also studied. Photodegradation reactions lead to the loss of many characteristic absorption bands and the apparition of new ones. To assess the specific fingerprints of different resins which do not depend on the degradation state, results were analysed by statistical treatment (Principal Component Analyses). This multi-disciplinary approach leads to the identification of new criterions including the decrease of specificity caused by the photochemical reactions. © 2013 Elsevier B.V.


Robin V.,University of Kiel | Talon B.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Nelle O.,University of Kiel
Quaternary International | Year: 2013

The notion of naturalness is an important concept of forest sustainable management, biological conservation, or as a base for restoration projects. The naturalness degree of a forest system is commonly evaluated based on forest ecology indicators, primarily with a relative short time resolution (e.g. dendroecological indication). However, the current state of ecological systems is the result of processes occurring in interaction at different and hierarchically connected spatial and temporal scales, including long term resolution (e.g. Holocene scale). Consequently, to assess the naturalness degree of ecological systems it is important to deal with their various temporal and spatial scales. In order to do that, palaeoecological approaches are needed, but hitherto have rarely been applied in naturalness investigations. The difficulties of interpretation in terms of spatial resolution of the main used palaeoecological approaches (e.g. palynology) and the presence of archive sites favourable to provide palaeoecological proxies seem to be limiting factors. Pedoanthracology allows the investigation of forest dynamics at the local spatial scale potentially everywhere, and for a longer time resolution. This paper illustrates this by using pedoanthracology to contribute to the naturalness assessment of three study cases in various biomes in Europe, in the south French Alps, in Central Germany and in Northern Germany. The charcoal richness of soil samples was quantified, and fragments were analysed taxonomically. Radiocarbon dating of single charcoals, combined with soil description, allows interpretation of the data within a temporal and spatial framework.At the site in Northern Germany, the ancient occurrence of fire was identified, burning early Holocene pioneer forest vegetation, while during more recent times, the burning of Fagus forest happened, Fagus sylvatica being today's dominant forest tree. At the site south of the Harz Mountains, in Central Germany, the established reference system is a Quercus dominated forest, which has persisted for thousands of years until today, possibly due to human woodland management. At the third site, in the French Southern Alps, the local forest system has never been more mature than in the current state, because it was regularly renewed by fire disturbances. © 2012 Elsevier Ltd and INQUA.


Lavrov D.V.,Iowa State University | Adamski M.,University of Bergen | Chevaldonne P.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Adamska M.,University of Bergen
Current Biology | Year: 2016

Summary One of the unusual features of DNA-containing organelles in general and mitochondria in particular is the frequent occurrence of RNA editing [1]. The term "RNA editing" refers to a variety of mechanistically unrelated biochemical processes that alter RNA sequence during or after transcription [2]. The editing can be insertional, deletional, or substitutional and has been found in all major types of RNAs [3, 4]. Although mitochondrial mRNA editing is widespread in some eukaryotic lineages [5-7], it is rare in animals, with reported cases limited both in their scope and in phylogenetic distribution [8-11] (see also [12]). While analyzing genomic data from calcaronean sponges Sycon ciliatum and Leucosolenia complicata, we were perplexed by the lack of recognizable mitochondrial coding sequences. Comparison of genomic and transcriptomic data from these species revealed the presence of mitochondrial cryptogenes whose transcripts undergo extensive editing. This editing consisted of single or double uridylate (U) insertions in pre-existing short poly(U) tracts. Subsequent analysis revealed the presence of similar editing in Sycon coactum and the loss of editing in Petrobiona massiliana, a hypercalcified calcaronean sponge. In addition, mitochondrial genomes of at least some calcaronean sponges were found to have a highly unusual architecture, with nearly all genes located on individual and likely linear chromosomes. Phylogenetic analysis of mitochondrial coding sequences revealed accelerated rates of sequence evolution in this group. The latter observation presents a challenge for the mutational-hazard hypothesis [13], which posits that mRNA editing should not occur in lineages with an elevated mutation rate. © 2016 Elsevier Ltd.


Weber A.A.T.,University of Geneva | Weber A.A.T.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Pawlowski J.,University of Geneva
Protist | Year: 2014

Ribosomal DNA is commonly used as a marker for protist phylogeny and taxonomy because of its ubiquity and its expected species specificity thanks to the mechanism of concerted evolution. However, numerous studies reported the occurrence of intragenomic (intra-individual) polymorphism in various protists and particularly in Foraminifera. To infer to what extent the SSU rDNA intragenomic variability occurs in Foraminifera, we studied 16 foraminiferal species belonging to single-chambered monothalamids and multi-chambered Globothalamea, with one to six individuals per species. We performed single-cell DNA extractions and PCRs of a 600. bp fragment of SSU rDNA, and sequenced 9 to 23 clones per individual for a total of 818 sequences. We found intragenomic variability in almost all species, even after excluding singleton mutations. Intra-individual sequence divergence ranged from 0 to 5.15% and was higher than 1% in 11 species. Variability was usually located at the end of stem-loop structures and included compensatory single nucleotide polymorphisms and expansion segments polymorphisms. However, the polymorphisms did not change the secondary structure of the rRNA. Our results suggest a non-concerted evolution of rRNA genes in Foraminifera. The origin of this variability and its implications for species identification in environmental DNA studies are discussed. © 2014 Elsevier GmbH.


Laureti L.,University of Paris Descartes | Selva M.,University of Paris Descartes | Selva M.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Dairou J.,University Paris Diderot | Matic I.,University of Paris Descartes
DNA Repair | Year: 2013

ATP is the most important energy source for the maintenance and growth of living cells. Here we report that the impairment of the aerobic respiratory chain by inactivation of the ndh gene, or the inhibition of glycolysis with arsenate, both of which reduce intracellular ATP, result in a significant decrease in spontaneous mutagenesis in Escherichia coli. The genetic analyses and mutation spectra in the ndh strain revealed that the decrease in spontaneous mutagenesis resulted from an enhanced accuracy of the replicative DNA polymerase. Quantification of the dNTP content in the ndh mutant cells and in the arsenate-treated cells showed reduction of the dNTP pool, which could explain the observed broad antimutator effects. In conclusion, our work indicates that the cellular energy supply could affect spontaneous mutation rates and that a reduction of the dNTP levels can be antimutagenic. © 2013 Elsevier B.V.


Malagnoux L.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental | Capowiez Y.,French National Institute for Agricultural Research | Rault M.,CNRS Mediterranean Institute for Biodiversity and Ecology Marine and Continental
Chemosphere | Year: 2014

Earwigs are important natural enemies of numerous pests in pome fruit orchards worldwide. Studying the effects of agricultural practices on these biological control agents is important for understanding its vulnerability in the field. The aim of this study was to characterize the B-esterase activities in the European earwig Forficula auricularia and to evaluate in vitro its sensitivity to organophosphate and carbamate pesticides. Acetylcholinesterase (AChE) activity was mainly measured with 1.5. mM acetylthiocholine as the substrate in the microsomal fraction of earwig heads (70% of total AChE activity). Carboxylesterase (CbE) activities were measured with three substrates [5. mM 4-nitrophenyl acetate (4-NPA), 1. mM 4-nitrophenyl valerate (4-NPV), and 2. mM α-naphtyl acetate (α-NA)] to examine different isoenzymes, which were present mainly in the cytosolic fraction (about 70-88% of total activities) of all earwig tissues. CbE activity was higher than AChE activity, especially with α-NA, then 4-NPA and lastly 4-NPV. Chlorpyrifos-oxon an organophosphate, and carbaryl a carbamate pesticide, inhibited AChE and CbE activities in a concentration-dependent manner. Earwig CbE activities showed a stronger sensitivity to organophosphate than AChE, with the strongest effect for chlorpyrifos-oxon on male carboxylesterase activities. CbE and AChE showed about the same sensitivity to carbamate pesticides regardless of sex. These results suggest that B-type esterases in the European earwig F. auricularia are suitable biomarkers of pesticide exposure. © 2014 Elsevier Ltd.

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