Using eDNA to detect the distribution and density of invasive crayfish in the Honghe-Hani rice terrace World Heritage site

The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish

Cloning and characterization of a novel oocyte-specific gene encoding an F-Box protein in rainbow trout (Oncorhynchus mykiss)

BACKGROUND: Oocyte-specific genes play critical roles in oogenesis, folliculogenesis and early embryonic development. The objectives of this study were to characterize the expression of a novel oocyte-specific gene encoding an F-box protein during ovarian development in rainbow trout, and identify its potential interacting partners in rainbow trout oocytes. METHODS: Through analysis of expressed sequence tags (ESTs) from a rainbow trout oocyte cDNA library, a novel transcript represented by ESTs only from the oocyte library was identified. The complete cDNA sequence for the novel gene (named fbxoo) was obtained by assembling sequences from an EST clone and a 5′RACE product. The expression and localization of fbxoo mRNA and protein in ovaries of different developmental stages were analyzed by quantitative real time PCR, immunoblotting, in situ hybridization and immunohistochemistry. Identification of Fbxoo binding proteins was performed by yeast two-hybrid screening. RESULTS: fbxoo mRNA is specifically expressed in mature oocytes as revealed by tissue distribution analysis. The fbxoo cDNA sequence is 1,996 bp in length containing an open reading frame, which encodes a predicted protein of 514 amino acids. The novel protein sequence does not match any known protein sequences in the NCBI database. However, a search of the Pfam protein database revealed that the protein contains an F-box motif at the N-terminus, indicating that Fbxoo is a new member of the F-box protein family. The expression of fbxoo mRNA and protein is high in ovaries at early pre-vitellogenesis stage, and both fbxoo mRNA and protein are predominantly expressed in early pre-vitellogenic oocytes. Several proteins including tissue inhibitor of metalloproteinase 2 (Timp2) were identified as potential Fbxoo protein binding partners. CONCLUSIONS: Results suggest that the novel oocyte-specific F-box protein may play an important role in early oocyte development by regulating other critical proteins involved in oogenesis in rainbow trout

Capture efficiency and size selectivity of sampling gears targeting red-swamp crayfish in several freshwater habitats

The ecological importance of the red-swamp crayfish (Procambarus clarkii) in the functioning of freshwater aquatic ecosystems is becoming more evident. It is important to know the limitations of sampling methods targeting this species, because accurate determination of population characteristics is required for predicting the ecological success of P. clarkii and its potential impacts on invaded ecosystems. In the current study, we addressed the question of trap efficiency by comparing population structure provided by eight trap devices (varying in number and position of entrances, mesh size, trap size and construction materials) in three habitats (a pond, a reed bed and a grassland) in a French marsh in spring 2010. Based on a large collection of P. clarkii (n = 2091, 272 and 213 respectively in the pond, reed bed and grassland habitats), we found that semi-cylindrical traps made from 5.5 mm mesh galvanized steel wire (SCG) were the most efficient in terms of catch probability (96.7–100% compared to 15.7–82.8% depending on trap types and habitats) and catch-per-unit effort (CPUE: 15.3, 6.0 and 5.1 crayfish·trap-1·24 h-1 compared to 0.2–4.4, 2.9 and 1.7 crayfish·trap-1·24 h-1 by the other types of fishing gear in the pond, reed bed and grassland respectively). The SCG trap was also the most effective for sampling all size classes, especially small individuals (carapace length \hbox{$\leqslant 30$} ⩽ 30 mm). Sex ratio was balanced in all cases. SCG could be considered as appropriate trapping gear to likely give more realistic information about P. clarkii population characteristics than many other trap types. Further investigation is needed to assess the catching effort required for ultimately proposing a standardised sampling method in a large range of habitats

FISH COMMUNITY STRUCTURE IN TEMPORARY LOWLAND FLOODED GRASSLANDS

In the context of a clear-cutting experiment of sedge areas on seasonally flooded grasslands, we described the fish community structure and the relationships between its spatial organisation and some environmental variables in early spring in 2000. A confinement gradient related to an increase in macrophyte density and determined by the nearest distance from permanent waters seemed to be a key factor in structuring the fish community in the flooded grasslands. Along this gradient, Cyprinids (essentially 0+) dominated near permanent water bodies (95% in abundance) but were substituted further by more tolerant species (Anguilla anguilla and Lepomis gibbosus) and mainly Ameiurus melas (age > 1, 40% in abundance). Although most species (10/13) present in the main permanent channels have been found in flooded grasslands, the efficiency of these grasslands as fish habitat was low compared to other similar sites from literature. We concluded on the importance of a confinement gradient and the water regime, isolating grasslands during summer and responsible of the scarce presence of fish

2007a) Fish emigration from temporary wetlands during drought: the role of physiological tolerance. Fundamental and Applied Limnology/Archiv für Hydrobiologie 168

Abstract: Fish emigration patterns from four temporary wetlands exposed to drought were studied from May to August 2004 in the Brière Marsh, France. Two wetlands became totally dry, and two experienced severe water level decline and significant changes in physico-chemical characters. Irrespective of the degree of desiccation, emigration patterns of the six most commonly trapped species, representing 98.6 % of the total abundance (Ameiurus melas, Anguilla anguilla, Scardinius erythrophthalmus, Lepomis gibbosus, Esox lucius and Gambusia holbrooki), were similar among wetlands. Emigration timing was highly correlated with published physiological tolerance levels for these species, demonstrating a tight linkage between water quality and emigration patterns. Two non-native species (A. melas and G. holbrooki) showed the latest emigration from the temporary habitats, reflecting a high level of tolerance to drought conditions that may contribute to their success as wetland invaders

Distribution and regulation of <em>Ludwigia grandiflora ssp.</em> <em>hexapetala</em> in the Natural Regional Park of Brière

International audienc

Fins are relevant non-lethal surrogates for muscle to measure stable isotopes in amphibians

Stable isotope analyses (SIA) are now widely used in ecology research to quantify the trophic implications of a large range of ecological processes. Non-destructive sampling methods have been successfully developed for most vertebrates, but the validation of such methods is missing in amphibians. Filling this methodological gap is critical to reduce the significant lack of knowledge on the trophic ecology of this imperilled group. The relevance of tail fin as a surrogate for muscle, a tissue routinely used for SIA, was assessed in four amphibian species, including tadpoles and adult newts, by (1) testing the link between the isotope ratios of carbon and nitrogen in fin and muscle, and addressing the additional practical issues of (2) the effects of a topical anaesthetic on isotope ratios, and (3) the minimum quantities of fin needed for SIA to limit the severity of sampling. The isotope ratios were highly correlated between the two tissues in all four species. Equations were provided to predict muscle estimates from fin values for each species separately and grouped by their taxonomic order (anurans or urodeles), which represent a valuable solution for any other species. Topical anaesthetics had little influence on isotope ratios, and the surface of tail fin needed for SIA was small. We conclude that the tail fin of amphibians can be used as a non-lethal surrogate for muscle in SIA, and this offers promising prospects for research on the trophic ecology of amphibians, and potentially on their conservation