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Sainte-Foy-lès-Lyon, France

Emmrich M.,Leibniz Institute of Freshwater Ecology and Inland Fisheries | Winfield I.J.,UK Center for Ecology and Hydrology | Guillard J.,French National Institute for Agricultural Research | Rustadbakken A.,Norwegian Institute for Water Research | And 11 more authors.
Freshwater Biology | Year: 2012

1. Sampling of lake fish assemblages is a challenging task in fish science, and the information obtained strongly depends on the choice of sampling gear. The use of more than one sampling technique is generally preferred in order to achieve a comprehensive view on fish assemblage structure. Therefore, the knowledge of whether catches between fishing gears are comparable is crucial. 2. We compared catches in benthic multi-mesh gillnets with fish biomass estimates obtained by vertical hydroacoustics in 18 European lakes strongly varying in morphometry and trophic status. Separate analyses were conducted for different depth strata and for several fish length thresholds to account for depth- and size-selective gillnet catches. 3. Gillnet catches and hydroacoustically obtained fish biomass estimates were significantly correlated. The strength of correlations was independent of the fish length thresholds applied, but varied across different depth strata of the lakes, with the strongest correlations occurring in the shallow strata. 4. The results support the applicability of vertical hydroacoustics for the quantification of fish biomass in stratified lakes. Survey designs combining hydroacoustics with limited gillnetting at sampling dates shortly one after the other, the latter for the purpose of inventory sampling only, are a cost-effective strategy for sampling fish assemblages in lakes. However, gillnet sampling does not provide reliable fish density estimates in very deep lakes with separate, pelagic-dwelling fish assemblages. © 2012 Blackwell Publishing Ltd. Source

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. Source

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. Source

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. Source

Le Cohu R.,Ecolab | Gassiole G.,ASCONIT Consultants | Coste M.,IRSTEA
Phytotaxa | Year: 2014

Recent surveys of the epilithic diatoms of Réunion Island led to the discovery of three new species: Crucicostulifera bebourensis, Encyonopsis cilaosensis, Encyonopsis palmeti. Crucicostulifera bebourensis is the second species to be included in this recently described genus typified by Crucicostulifera areolata (Hustedt) Taylor & Lange-Bertalot. Both species share the main diagnostic features of the genus. However, Crucicostulifera bebourensis differs from Crucicostulifera areolata (Hustedt) Taylor & Lange-Bertalot in the cingulum composed of at least three open bands whereas the latter species has a single valvocopula on each valve. Encyonopsis cilaosensis and Encyonopsis palmeti can be differentiated from other Encyonopsis species by a combination of characters including valve outline, number of striae in l0 μm, maximum length/breadth ratio, areolae structure and presence or absence of intermissio. Both new species show a particular organization of the cingulum. Crucicostulifera bebourensis occurs in acidic waters with very low conductivity and nutrient concentration. Encyonopsis cilaosensis is found in alkaline waters with high conductivity whereas Encyonopsis palmeti is reported from slighty alkaline waters with low conductivity. © 2014 Magnolia Press. Source

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