Sainte-Foy-lès-Lyon, France
Sainte-Foy-lès-Lyon, France

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Rimet F.,French National Institute for Agricultural Research | Trobajo R.,Institute of Agriculture and Food Research and Technology | Mann D.,Royal Botanic Garden Edinburgh | Kermarrec L.,Asconit Consultants | And 3 more authors.
Protist | Year: 2014

DNA barcoding, being developed for biomonitoring, requires a database of reference sequences and knowledge of how much sequences can deviate before they are assigned to separate species. The molecular hunt for hidden species also raises the question of species definitions. We examined whether there are objective criteria for sequence-based species delimitation in diatoms, using Nitzschia palea, an important monophyletic indicator species already known to contain cryptic diversity. Strains from a wide geographical range were sequenced for 28S rRNA, COI and rbcL. Homogeneity indices and the Chao index failed to objectively select a precise number of species existing in N. palea as well as an evolutionary method based on coalescence theory. COI always gave higher diversity estimations than 28S rRNA or rbcL. Mating data did not provide a precise calibration of molecular species thresholds. Rarefaction curves indicated that further MOTUs would be detected with more isolates than we sampled (81 clones, 42 localities). Although some genotypes had intercontinental distributions, there was a positive relationship between genetic and geographical distance, suggesting even higher richness than we assessed, given that many regions were not sampled. Overall, no objective criteria were found for species separation; instead barcoding will need a consensual approach to molecular species limits. © 2014 Elsevier GmbH.


Larroude S.,French National Institute for Agricultural Research | Massei N.,University of Rouen | Reyes-Marchant P.,ASCONIT Consultants | Delattre C.,Électricité de France | Humbert J.F.,French National Institute for Agricultural Research
Global Change Biology | Year: 2013

The impact of climate change and of other anthropogenic pressures on the structure and composition of phytoplankton communities of large European rivers remains poorly documented. Here we report the findings of a study of the changes in the phytoplankton community of the middle segment of the river Loire over the past 24 years. An attempt is made to distinguish between the impact of changes acting at the local scale and that of those acting more globally. A dramatic reduction in phytoplankton abundance was observed, particularly in the mid -1990s; this was concomitant with an increase in the relative proportion of cyanobacteria. At the same time, the phytoplankton community displayed increasing richness and diversity, and little change in its size structure. All these changes seem to be related to local changes, in particular to the reduction in phosphorus concentrations, as well as to changes in climate, throughout modifications in the river discharge and water temperature. Interestingly, herbicide contamination also appeared to be of particular importance in explaining the unexpected increase in the proportion of cyanobacteria in the phytoplankton community after the 1990s. These findings suggest that combinations of numerous anthropogenic pressures acting at different spatial and temporal scales have led to a mix of predictable and unpredictable changes occurring in the phytoplankton community of the river Loire, with probable consequences for the trophic networks in this river. © 2013 Blackwell Publishing Ltd.


Martignac F.,ASCONIT Consultants | Bagliniere J.L.,French National Institute for Agricultural Research | Thieulle L.,ASCONIT Consultants | Ombredane D.,French National Institute for Agricultural Research | Guillard J.,French National Institute for Agricultural Research
Estuarine, Coastal and Shelf Science | Year: 2013

A dam has been recently modified on the Couesnon River in the vicinity of Mont Saint Michel to control and remove the volume of sediment brought into the bay by tidal waters. This paper shows that this dam has an impact on Atlantic salmon (Salmo salar) migration and that adult fish experience adaptive responses. Upstream migration activities were recorded with a 70kHz echosounder (SIMRAD EY500 model) during two monitoring programs in 2010 and 2011, combining a total of 172 days of data collection. The echosounder was fixed at an upstream location, 8km from the dam, and its detection beam capacity was approximately one third of the river's cross sectional area. In addition to the time of year, the upstream direction, swimming speed limit and fish size range were the specific criteria used from our database to efficiently discriminate other fish species from the Atlantic salmon. Among a total of 116,000 fishes counted during the two periods of investigations, 189 salmon were identified using those criteria. This study enabled us to identify the driving factors that influence the salmon migration in this semi-natural environment. There was a significant difference in fish activity when the dam was operating and when the river flow was under "normal" hydraulic conditions.Furthermore, during the opening and closing phases of the dam, the migration activity was scattered during the day, with peak abundance occurring mainly during the beginning of the operating phases. However, during all valve-opening phases, the salmon activity occurred mainly during the night. Therefore, the results suggest that this dam has a strong influence on fish migration activity at this particular location. © 2013 Elsevier Ltd.


Peres F.,Asconit Consultants | Le Cohu R.,University Paul Sabatier | Delmont D.,DREAL Languedoc Roussillon
Diatom Research | Year: 2014

Two new benthic freshwater species belonging to the genus Achnanthidium Kützing were found in French rivers located in the Languedoc-Roussillon region. Achnanthidium barbei and A. costei are described as new species based on light and scanning electron microscopy observations. These species belong to the A. minutissimum complex based on the short, straight distal raphe fissures. Achnanthidium barbei and A. costei were found in rivers characterized by an alkaline pH and high phosphorus. Achnanthidium costei occurs in waters with very high conductivity and sulfate. The most characteristic morphological features of A. barbei are the bent frustule with recurved apices in girdle view, clearly lanceolate valves with convex margins and distinctly protracted apices, and the presence of up to six areolae per stria. Achnanthidium costei is characterized by a linear raphe valve outline and a wide axial area on the rapheless valve. Both species are compared with the most similar species: A. caravelense Novais & Ector, A. ennediense (Compère) Compère & Van de Vijver, A. eutrophilum (Lange-Bertalot) Lange-Bertalot, A. lineare W. Smith, A. minutissimun (Kützing) Czarnecki., A. pseudolineare Van de Vijver, Novais & Ector, A. sublineare Van de Vijver, Novais & Ector and A. tepidaricola Van de Vijver & M. de Haan. The ecological preferences of both species are assessed based on physicochemical analyses carried out on sites that are part of water quality monitoring networks. © 2014 The International Society for Diatom Research.


Martignac F.,ASCONIT Consultants | Martignac F.,Agrocampus Ouest | Daroux A.,Agrocampus Ouest | Bagliniere J.-L.,Agrocampus Ouest | And 2 more authors.
Fish and Fisheries | Year: 2015

European Union legislation, through the Water Framework Directive (2000/60/EC), as well as national legislation, such as the 'Grenelle Environnement' (2007) in France, requires restoration of ecological connectivity in streams to improve free circulation of migratory fish. Different methods (e.g. capture by trap or net, telemetry, hydroacoustics) are used to evaluate the efficiency of fish passes to estimate the migratory species abundance and analyse changes in their within-river distributions. Among these methods, hydroacoustics is non-intrusive, allowing long-term observation and description of fish populations based on physical properties of sound in water. However, the main limit to hydroacoustic tools is their difficulty in identifying species. Initially designed for military purposes, dual-frequency identification sonar (DIDSON) has been used in environmental management for a decade. This acoustic camera uses higher frequencies and more sub-beams than common hydroacoustic tools, which improves image resolution and then enables observation of fish morphology and swimming behaviour. The ability to subtract static echoes from echograms and directly measure fish length improve the species-identification process. However, some limits have been identified, such as automatic dataset recording and the low range of the detection beam, which decreases accuracy, but efficient tools are now being developed to improve the accuracy of data recording (morphology, species identification, direction and speed). The new technological properties of acoustic cameras, such as the video-like visualization of the data, have greatly improved monitoring of diadromous fish populations (abundance, distribution and behaviour), helping river and fisheries managers and researchers in making decisions. © 2014 John Wiley & Sons Ltd.


PubMed | ASCONIT Consultants, Swedish University of Agricultural Sciences, University of Savoy and University of Bordeaux 1
Type: | Journal: Database : the journal of biological databases and curation | Year: 2016

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst.inra.fr/.


Girard V.,IRSTEA | Monti D.,University of the French West Indies and Guiana | Valade P.,Center Regional dApplication Aquacole | Lamouroux N.,IRSTEA | And 2 more authors.
River Research and Applications | Year: 2014

Hydraulic habitat models based on the preferences of species for the hydraulic characteristics of their microhabitats are frequently used to evaluate the impact on the habitat of a change in river flow regime. Their application in a tropical insular environment is still limited as little is known about the hydraulic preferences of species. Hydraulic preference models have been developed for 15 taxa (diadromous shrimps and fishes) sampled in 52 rivers in the Caribbean (the French West Indies) and the Indian Ocean (the Reunion island). Five datasets were used and group 8353 samples collected by electrofishing during 320 surveys (reach×date) performed between 1999 and 2011. Generalized additive models were used to link variations of taxa density within surveys to the hydraulic characteristics of the microhabitat (velocity, depth and substrate). Hydraulic preferences within each region (Caribbean and Indian Ocean) are significant for most of the taxa and vary little between rivers and surveys. The hydraulic variables explain up to 18.1% (univariate models) and 30.0% (multivariate models) of the deviance of densities within survey. Of the taxa selected, Atya scabra, Macrobrachium heterochirus, Xiphocaris elongata and the Sicydiinae are the most demanding. © 2013 John Wiley & Sons, Ltd.


Desrosiers C.,CNRS Functional Ecology & Environment Laboratory | Leflaive J.,CNRS Functional Ecology & Environment Laboratory | Eulin A.,Asconit Consultants | Ten-Hage L.,CNRS Functional Ecology & Environment Laboratory
Ecological Indicators | Year: 2013

Marine waters in general and coastal areas in particular suffer globally from stressing events. These events can be largely attributed to higher levels of human-induced eutrophication, contamination by pollutant, and siltation. The European Union and other countries have adopted legislation to guide monitoring efforts and set goals for good quality coastal environments. Few biological quality elements were identified by legislators for their ability to detect and identify sources of ecosystem perturbations. Research programs have developed indices calculation methods for benthic invertebrate fauna, phytoplankton, macroalgae and angiosperms. Most of these indices are multimetric, based on the richness, abundance and biomass of the community. Such indices determine the quality at one site after observational comparison with a reference situation. Functional indices, however, are based on species ecological preferenda and autoecology. Since species are generally response-specific, functional index allows the discernment of the stressing factor involved in the ecosystem perturbation. The final index value provides a direct appreciation of the ecological status of the study site. At the present time, there are few functional indices that can be used on a routine basis for monitoring coastal waters. Because biological quality elements cited below are not available in all areas, the range of monitoring is restricted to particular environments. This review paper suggests that marine benthic diatoms (Bacillariophyceae) may result in a functional index. Arguments for the use of these organisms as bio-indicators include knowledge from the past and present use of diatoms in freshwater environmental analysis. Marine benthic diatoms are abundant and ubiquitous in terms of ecosystems and water chemistry and are sensitive to nutrient variation, as revealed by two studies conducted in mesotrophic and oligotrophic areas. This review is focused on benthic diatoms and reveals that no study has yet been conducted on the use of these organisms as bio-indicators. Aspects of practical sampling and sample treatment for marine diatoms are considered. As the bio-indication role of diatoms is little explored in marine environments, the dataset on ecological indicator values of species is scarce. Future work that relates to taxonomic determination and physico-chemical description of sites are needed to better define species ecological preferenda, prior to the development of a marine diatom biotic index. © 2013 Elsevier Ltd.


Le Cohu R.,Ecolab | Barthes A.,ASCONIT Consultants | LeflLaive J.,Ecolab | Ten-Hage L.,Ecolab
Fottea | Year: 2016

A species new to science, Germainiella clandestina, was discovered during experiments performed in an artificial freshwater channel. This species is described based on valve morphology typical for the genus Germainiella Lange-BertalLot et MetzelLtin. The major features conforming to Germainiella are the valve face as well as a part of the mantle covered by a conopeum and the presence of very small apertures corresponding to a subconopeum canal system close to the raphe fissure. These characters clearly differentiate this taxon from the two more related genera, namely Fallacia SsticCklLe et Mann and Pseudofallacia occulta (Kkrasske) Y. Liu, J.P. KkocCiolLek et Q.X. Wang. Moreover, two chloroplasts could be observed for the first time in Germainiella, providing an additional feature to separate Germainiella and both genera cited above. Some information is given on its ecology. © Czech Phycological Society (2016).


Desrosiers C.,University Paul Sabatier | Leflaive J.,University Paul Sabatier | Eulin A.,Asconit Consultants | Ten-Hage L.,University Paul Sabatier
Journal of Applied Phycology | Year: 2014

Benthic diatoms growing on hard substrata are used for their bioindication ability in freshwater quality monitoring. Artificial substrata are needed in cases where any natural substrate is present or to achieve similar sampling conditions between sites. Prior to use marine benthic diatoms for monitoring, a standardized protocol for sampling on artificial substrata must be set up. Two major types of information are required: (1) the time needed for a diatom community to be well developed and mature (climax stage); (2) the optimal growth conditions, given that the substrataum nature and texture are important parameters for the initial phase of biofilm development and can influence the future diatom assemblage. Three substrataum types were tested: frosted Plexiglass®, frosted glass, and rough enameled tiles. They were submerged for 8 weeks and sampled weekly. The experiment was conducted at five sites of distinct morphology and water chemistry, along the coastal area of Martinique Island, French West Indies. Development of diatom community was studied through biofilm dry weight, valve density, species richness, and species relative abundances. Globally, substratum type had no significant effect on any parameter. Frosted Plexiglass® was found to be the most interesting substratum because of higher valve densities and practical use. The asymptotic phase of biofilm development was encountered between 5 and 8 weeks depending on site and parameter. A compromise between community development and vandalism or loss through time was fixed to 5 weeks. This period is longer than for stream environments and is valid for tropical oligotrophic marine environments. © 2013 Springer Science+Business Media Dordrecht.

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