95 research outputs found
Molecular Detection of Invasive Species in Heterogeneous Mixtures Using a Microfluidic Carbon Nanotube Platform
Screening methods to prevent introductions of invasive species are critical for the protection of environmental and economic benefits provided by native species and uninvaded ecosystems. Coastal ecosystems worldwide remain vulnerable to damage from aquatic species introductions, particularly via ballast water discharge from ships. Because current ballast management practices are not completely effective, rapid and sensitive screening methods are needed for on-site testing of ships in transit. Here, we describe a detection technology based on a microfluidic chip containing DNA oligonucleotide functionalized carbon nanotubes. We demonstrate the efficacy of the chip using three ballast-transported species either established (Dreissena bugensis) or of potential threat (Eriocheir sinensis and Limnoperna fortuneii) to the Laurentian Great Lakes. With further refinement for on-board application, the technology could lead to real-time ballast water screening to improve ship-specific management and control decisions
Estimation of Fish Biomass Using Environmental DNA
Environmental DNA (eDNA) from aquatic vertebrates has recently been used to estimate the presence of a species. We hypothesized that fish release DNA into the water at a rate commensurate with their biomass. Thus, the concentration of eDNA of a target species may be used to estimate the species biomass. We developed an eDNA method to estimate the biomass of common carp (Cyprinus carpio L.) using laboratory and field experiments. In the aquarium, the concentration of eDNA changed initially, but reached an equilibrium after 6 days. Temperature had no effect on eDNA concentrations in aquaria. The concentration of eDNA was positively correlated with carp biomass in both aquaria and experimental ponds. We used this method to estimate the biomass and distribution of carp in a natural freshwater lagoon. We demonstrated that the distribution of carp eDNA concentration was explained by water temperature. Our results suggest that biomass data estimated from eDNA concentration reflects the potential distribution of common carp in the natural environment. Measuring eDNA concentration offers a non-invasive, simple, and rapid method for estimating biomass. This method could inform management plans for the conservation of ecosystems
A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant
Path segmentation for beginners: an overview of current methods for detecting changes in animal movement patterns
Hemispheric differences between left and right supramarginal gyrus for pitch and rhythm memory
Functional brain imaging studies and non-invasive brain stimulation methods have shown the importance of the left supramarginal gyrus (SMG) for pitch memory. The extent to which this brain region plays a crucial role in memory for other auditory material remains unclear. Here, we sought to investigate the role of the left and right SMG in pitch and rhythm memory in non-musicians. Anodal or sham transcranial direct current stimulation (tDCS) was applied over the left SMG (Experiment 1) and right SMG (Experiment 2) in two different sessions. In each session participants completed a pitch and rhythm recognition memory task immediately after tDCS. A significant facilitation of pitch memory was revealed when anodal stimulation was applied over the left SMG. No significant effects on pitch memory were found for anodal tDCS over the right SMG or sham condition. For rhythm memory the opposite pattern was found; anodal tDCS over the right SMG led to an improvement in performance, but anodal tDCS over the left SMG had no significant effect. These results highlight a different hemispheric involvement of the SMG in auditory memory processing depending on auditory material that is encoded
The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain
[EN] Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.This project has been supported by the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (EUPHRESCO-CEP: "Current and Emerging Phytophthoras: Research Supporting Risk Assessment And Risk Management"). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Català, S.; Pérez Sierra, AM.; Abad Campos, P. (2015). The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain. 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Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest. Fungal Ecology, 6(3), 223-235. doi:10.1016/j.funeco.2013.01.002Vannini, A., Bruni, N., Tomassini, A., Franceschini, S., & Vettraino, A. M. (2013). Pyrosequencing of environmental soil samples reveals biodiversity of thePhytophthoraresident community in chestnut forests. FEMS Microbiology Ecology, 85(3), 433-442. doi:10.1111/1574-6941.12132Jerde, C. L., Mahon, A. R., Chadderton, W. L., & Lodge, D. M. (2011). «Sight-unseen» detection of rare aquatic species using environmental DNA. Conservation Letters, 4(2), 150-157. doi:10.1111/j.1755-263x.2010.00158.xMonchy, S., Sanciu, G., Jobard, M., Rasconi, S., Gerphagnon, M., Chabé, M., … Sime-Ngando, T. (2011). Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing. 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Cosmopolitanism of microbial eukaryotes in the global deep seas. Molecular Ecology, 21(5), 1033-1035. doi:10.1111/j.1365-294x.2012.05437.xDavey, M. L., Heegaard, E., Halvorsen, R., Kauserud, H., & Ohlson, M. (2012). Amplicon-pyrosequencing-based detection of compositional shifts in bryophyte-associated fungal communities along an elevation gradient. Molecular Ecology, 22(2), 368-383. doi:10.1111/mec.12122Weber, C. F., Vilgalys, R., & Kuske, C. R. (2013). Changes in Fungal Community Composition in Response to Elevated Atmospheric CO2 and Nitrogen Fertilization Varies with Soil Horizon. Frontiers in Microbiology, 4. doi:10.3389/fmicb.2013.00078Bergmark, L., Poulsen, P. H. B., Al-Soud, W. A., Norman, A., Hansen, L. H., & Sørensen, S. J. (2012). Assessment of the specificity of Burkholderia and Pseudomonas qPCR assays for detection of these genera in soil using 454 pyrosequencing. 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Quantification of Phytophthora capsici Oospores in Soil by Sieving-Centrifugation and Real-Time Polymerase Chain Reaction. Plant Disease, 92(1), 143-149. doi:10.1094/pdis-92-1-0143Than, D. J., Hughes, K. J. D., Boonhan, N., Tomlinson, J. A., Woodhall, J. W., & Bellgard, S. E. (2013). A TaqMan real-time PCR assay for the detection ofPhytophthora‘taxon Agathis’ in soil, pathogen of Kauri in New Zealand. Forest Pathology, 43(4), 324-330. doi:10.1111/efp.12034Chen, W., Djama, Z. R., Coffey, M. D., Martin, F. N., Bilodeau, G. J., Radmer, L., … Lévesque, C. A. (2013). Membrane-Based Oligonucleotide Array Developed from Multiple Markers for the Detection of Many Phytophthora Species. Phytopathology, 103(1), 43-54. doi:10.1094/phyto-04-12-0092-rScibetta, S., Schena, L., Chimento, A., Cacciola, S. O., & Cooke, D. E. L. (2012). A molecular method to assess Phytophthora diversity in environmental samples. 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Recruitment sources of invasive Bighead carp (Hypopthalmichthys nobilis) and Silver carp (H. molitrix) inhabiting the Illinois River
Environmental DNA (eDNA) detects the invasive crayfishes Orconectes rusticus and Pacifastacus leniusculus in large lakes of North America
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