Download or read book Assessing the Persistence of Environmental DNA and Environmental RNA for Zooplankton Biodiversity Monitoring by Metabarcoding written by Anna Harris and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "Environmental DNA (eDNA) metabarcoding has proven successful at detecting low abundance species due to the stability and ubiquity of DNA in the environment. While this is ideal for efficient monitoring over large geographic ranges, eDNA persistence and transport within aquatic systems often introduces false positive detection of species which are spatially or temporally removed. Environmental RNA (eRNA) metabarcoding may allow better spatial and temporal resolution by detecting only present, local species due to the faster degradation rate of the RNA molecule; however, little is known about eRNA persistence in the environment. Here I test species detection in zooplankton communities using eDNA and eRNA metabarcoding of two barcode markers (COI and 18S) across seven time points spanning from one hour to one month after organism removal. The metabarcoding results were validated with morphologically identified voucher specimens and mock communities. Community composition as detected by eDNA and eRNA was similar, however, species assignment at the COI and 18S markers differed. Zooplankton were detectable with eDNA throughout the experiment with the COI marker and at all but one time point with the 18S marker, whereas detection with eRNA ceased at 24 hours after organism removal for both markers, with only rare detections at 48 hours with 18S, and four and seven days with COI. There was an unexpected increase in detection at the 28-day time point for all methods, possibly due to concentration of eDNA and eRNA adhered to the container walls. Through comparing the two metabarcoding techniques, I have demonstrated that eRNA metabarcoding stops detecting zooplankton species shortly after organism removal, while detection by eDNA metabarcoding persists for at least seven days. Environmental RNA metabarcoding could be applied in parallel with eDNA metabarcoding to distinguish current, local diversity, which is particularly relevant for high-resolution sampling, such as for species at risk or invasive species monitoring. " --
Download or read book Environmental DNA written by Pierre Taberlet and published by Oxford University Press. This book was released on 2018-02-02 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Environmental DNA (eDNA) refers to DNA that can be extracted from environmental samples (such as soil, water, feces, or air) without the prior isolation of any target organism. The analysis of environmental DNA has the potential of providing high-throughput information on taxa and functional genes in a given environment, and is easily amenable to the study of both aquatic and terrestrial ecosystems. It can provide an understanding of past or present biological communities as well as their trophic relationships, and can thus offer useful insights into ecosystem functioning. There is now a rapidly-growing interest amongst biologists in applying analysis of environmental DNA to their own research. However, good practices and protocols dealing with environmental DNA are currently widely dispersed across numerous papers, with many of them presenting only preliminary results and using a diversity of methods. In this context, the principal objective of this practical handbook is to provide biologists (both students and researchers) with the scientific background necessary to assist with the understanding and implementation of best practices and analyses based on environmental DNA.
Download or read book Evaluating Environmental DNA eDNA Metabarcoding as a Method for Monitoring Biodiversity in Marine Ecosystems written by Gert-Jan Jeunen and published by . This book was released on 2018 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt: 3) I determined the influence of water column stratification on the ability of eDNA metabarcoding surveys to uncover subtidal biodiversity patterns in marine systems. Comparing eDNA signals between non-mixing water layers showed highly distinct patterns, while similar eDNA signals were obtained in areas subject to vertical water displacement. Based on these results, I advocate to take into consideration the oceanographic processes within an area when designing eDNA sampling strategies in marine ecosystems.
Download or read book River Networks as Ecological Corridors written by Andrea Rinaldo and published by Cambridge University Press. This book was released on 2020-10-22 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: A summary of state-of-the-art research on how the river environment impacts biodiversity, species invasions, population dynamics, and the spread of waterborne disease. Blending laboratory, field and theoretical studies, it is the go-to reference for graduate students and researchers in river ecology, hydrology, and epidemiology.
Download or read book Applicability of EDNA and ERNA in Assessing Species and Community Composition Across an Acid base Gradient in Freshwater Environments written by Kaushar Kagzi and published by . This book was released on 2022 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: "The use and development of biomonitoring tools based on environmental nucleic acids (eNAs) have gained considerable interest for biodiversity characterization in freshwater ecosystems. However, the applicability of any biomonitoring tool is dependent upon both an understanding of its inherent biases and limitations, as well as knowledge of environmental factors influencing the detectability of target organisms. Although there is a growing body of research dedicated to evaluating the impacts of various environmental parameters on the ecology of environmental DNA (eDNA), knowledge of how these factors impact the ecology of environmental RNA (eRNA) in aquatic systems is severely limited. This thesis aims to improve our collective understanding of the influence of site-specific environmental parameters on the ecology (i.e. degradation and persistence dynamics) and performance of eNA-based survey methods, with a focus on the acidity of the sampled environment. Using artificial freshwater mesocosms, I first use eNA metabarcoding of the cytochrome c oxidase subunit I (COI) gene to assess: a) how eNA-based survey results compare to traditional morphology-based methods in quantifying zooplankton diversity; b) the accuracy of eDNA and eRNA in capturing species turnover in response to a severe acid stressor; and c) how site-specific pH influences eDNA and eRNA yield. I then use a droplet digital PCR assay targeting the COI gene region of the zooplankton Daphnia pulex to evaluate the significance of pH on eDNA and eRNA persistence and decay rates over time. Collectively, I find that eNA-based survey results are more similar to one another than to those obtained using traditional methods. In addition, I demonstrate that eRNA provides a finer spatio-temporal inference of current, living species assemblages and captures species turnover more rapidly than eDNA in response to environmental stress. I also show that eDNA/eRNA decay rates, yield and persistence dynamics may differ depending on the pH of the sampled environment. Altogether, these results may be used to inform eNA-based sampling design and survey methods, and consequently improve upon the collection and evaluation of biodiversity data"--
Download or read book DNA metabarcoding written by Jerney, Jacqueline and published by Nordic Council of Ministers. This book was released on 2023-04-12 with total page 68 pages. Available in PDF, EPUB and Kindle. Book excerpt: We present guidelines for using environmental DNA metabarcoding, together with conventional techniques, to monitor the taxonomic diversity of phytoplankton in marine and brackish waters. The focus is on eukaryotic and prokaryotic phytoplankton using 18S and 16S rRNA primers and high-throughput sequencing. Information and recommendations on sampling, sample processing, molecular biological work, quality control, bioinformatics, data storage and management and cost estimates are included so that the method can be used to complement standardized light microscopy. A scientific literature review, discussion on future perspectives, reference databases and standardization are included. Using eDNA metabarcoding to complement standardized light microscopy advances conventional monitoring and research on phytoplankton communities to assess biodiversity and the state of the marine environment.
Download or read book The Use of Environmental DNA in Evaluating Conservation Efforts Within Southern California s Marine Waters written by Tanner Anthony Waters and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Environmental DNA metabarcoding (eDNA) is an evolving methodology of biodiversity monitoring. By leveraging shed and excreted DNA from organisms in a marine environment, researchers can perform DNA amplification and sequencing to identify what species were present at a site without the need for visual identification. This thesis uses eDNA to evaluate conservation efforts in Southern California as well as further establish and refine eDNA as a survey tool. In Chapter 1, I evaluate seagrass beds in three distinct geographic settings in Southern California. We demonstrate that nearly half of community composition is associated with whether seagrass was found off the mainland, off an island, or in an embayment. In addition, when compared to traditional monitoring, eDNA was able to identify roughly ~50% to 400% greater number of fish species at each site. In Chapter 2, I create a novel eDNA droplet digital PCR assay for the detection of the invasive species Caulerpa prolifera that was found in Newport Bay in 2021 and found it to have the lowest eDNA steady state of any previously tested species. We demonstrate the critical importance of benchmarking eDNA assays before their use by managers and highlight some limitations for using eDNA in species detection. In Chapter 3, we perform two years of monthly sampling of MPAs using community scientists and UCLA researchers. We find that MPAs are distinct from nonMPAs in multivariate space for both fish and metazoan communities and that metazoan communities in MPAs are more diverse and stable compared to nonMPAs. We also show the scalability that eDNA has in biodiversity monitoring through the incorporation of volunteers into field sampling. Together, these chapters better our understanding of marine conservation in Southern California and further demonstrate the utility and limitations of eDNA metabarcoding for monitoring marine biodiversity.
Download or read book Marine Metagenomics written by Takashi Gojobori and published by Springer. This book was released on 2019-07-24 with total page 271 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the state-of-art marine metagenome research and explains the method of marine metagenomic analysis in an easy-to-understand manner. Changes in the marine environment due to global warming and pollution have become a major global problem. Maintaining a healthy marine ecosystem requires advanced environmental monitoring and assessment systems. As such, the book presents a novel metagenomic monitoring method, which has been developed for comprehensive analyses of the DNA of microorganisms living in seawater to further our understanding of the dynamics of the marine environment. The book can be used as a primer for new researchers and as a manual on experimental methods.
Download or read book Intermittent Rivers and Ephemeral Streams written by Thibault Datry and published by Academic Press. This book was released on 2017-07-11 with total page 624 pages. Available in PDF, EPUB and Kindle. Book excerpt: Intermittent Rivers and Ephemeral Streams: Ecology and Management takes an internationally broad approach, seeking to compare and contrast findings across multiple continents, climates, flow regimes, and land uses to provide a complete and integrated perspective on the ecology of these ecosystems. Coupled with this, users will find a discussion of management approaches applicable in different regions that are illustrated with relevant case studies. In a readable and technically accurate style, the book utilizes logically framed chapters authored by experts in the field, allowing managers and policymakers to readily grasp ecological concepts and their application to specific situations. - Provides up-to-date reviews of research findings and management strategies using international examples - Explores themes and parallels across diverse sub-disciplines in ecology and water resource management utilizing a multidisciplinary and integrative approach - Reveals the relevance of this scientific understanding to managers and policymakers
Download or read book Lake Restoration Handbook written by David P. Hamilton and published by Springer. This book was released on 2019-01-29 with total page 603 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lakes across the globe require help. The Lake Restoration Handbook: A New Zealand Perspective addresses this need through a series of chapters that draw on recent advances in modelling and monitoring tools, citizen science and First Peoples’ roles, catchment and lake-focused restoration techniques, and policy implementation. New Zealand lakes, like lakes across the globe, are subject to multiple pressures that have increased in severity and scale as land use has intensified, invasive species have spread and global climate change becomes manifest. This books builds on the popular Lake Managers Handbook (1987), which provided guidance on undertaking investigations into, and understanding lake ecosystems in New Zealand. The Lake Restoration Handbook: A New Zealand Perspective synthesises contemporary issues related to lake restoration and rehabilitation, integrated with social science and cultural viewpoints, and complemented by authoritative topic-area summaries by renowned scientists and practitioners from across the globe. The book examines the progress of lake restoration and the new and emerging tools available to managers for predicting and effecting change. The book will be a valuable resource for natural and social scientists, policy writers, lake managers, and anyone interested in the health of lake ecosystems.
Download or read book Coastal lagoons written by Pierre Lasserre and published by . This book was released on 1982 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Freshwater Biodiversity written by David Dudgeon and published by Cambridge University Press. This book was released on 2020-05-21 with total page 517 pages. Available in PDF, EPUB and Kindle. Book excerpt: Growing human populations and higher demands for water impose increasing impacts and stresses upon freshwater biodiversity. Their combined effects have made these animals more endangered than their terrestrial and marine counterparts. Overuse and contamination of water, overexploitation and overfishing, introduction of alien species, and alteration of natural flow regimes have led to a 'great thinning' and declines in abundance of freshwater animals, a 'great shrinking' in body size with reductions in large species, and a 'great mixing' whereby the spread of introduced species has tended to homogenize previously dissimilar communities in different parts of the world. Climate change and warming temperatures will alter global water availability, and exacerbate the other threat factors. What conservation action is needed to halt or reverse these trends, and preserve freshwater biodiversity in a rapidly changing world? This book offers the tools and approaches that can be deployed to help conserve freshwater biodiversity.
Download or read book Monitoring Freshwater Fish Communities with Environmental DNA eDNA Metabarcoding written by Jonas Bylemans and published by . This book was released on 2018 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: "Efficient monitoring and management of species biodiversity requires sensitive and reliable detection tools, especially when management focusses on species that are present at low densities. Recent technological advances now allow biodiversity to be monitored through the DNA that organisms leave behind in the environment (eDNA). These eDNA-based tools are less susceptible to biases and can significantly improve the data from monitoring surveys, which in turn leads to a better management of natural resources. The aim of this thesis is to examine the potential of different DNA fragments for eDNA-based monitoring and evaluate the potential of eDNA metabarcoding as a monitoring tool for freshwater fish communities within the Murray-Darling Basin (MDB, Australia)."
Download or read book Time Series Experiments Reveal that Environmental DNA Tracks Zooplankton Population Dynamics in Large Mesocosms written by Danielle Bourque and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Environmental DNA (eDNA) holds great potential for biomonitoring and ecological research. However, its utility for quantifying temporal changes in abundance, biomass, and diversity remains contentious. In this thesis, I investigated biotic and abiotic factors influencing temporal and spatial variation in eDNA concentration. Time series data demonstrated a positive relationship between the population abundance of the cladoceran zooplankton species Daphnia magna and its eDNA concentration in large aquatic mesocosms, with a time lag of ~ 3.5 days. Environmental temperatures of 15 °C promoted greater eDNA persistence than metabolically favorable (25 °C) conditions. Levels of spatial autocorrelation suggest that the swimming activity of Daphnia and/or thermally-driven mixing might have homogenized the distribution of their eDNA over the entire water column.
Download or read book ICES Zooplankton Methodology Manual written by Roger Harris and published by Elsevier. This book was released on 2000-02-14 with total page 707 pages. Available in PDF, EPUB and Kindle. Book excerpt: The term "zooplankton" describes the community of floating, often microscopic, animals that inhabit aquatic environments. Being near the base of the food chain, they serve as food for larger animals, such as fish. The ICES (International Council for the Exploration of the Sea) Zooplankton Methodology Manual provides comprehensive coverage of modern techniques in zooplankton ecology written by a group of international experts. Chapters include sampling, acoustic and optical methods, estimation of feeding, growth, reproduction and metabolism, and up-to-date treatment of population genetics and modeling. This book will be a key reference work for marine scientists throughout the world. - Sampling and experimental design - Collecting zooplankton - Techniques for assessing biomass and abundance - Protozooplankton enumeration and biomass estimation - New optical and acoustic techniques for estimating zooplankton biomass and abundance - Methods for measuring zooplankton feeding, growth, reproduction and metabolism - Population genetic analysis of zooplankton - Modelling zooplankton dynamics This unique and comprehensive reference work will be essential reading for marine and freshwater research scientists and graduates entering the field.
Download or read book Environmental DNA as a Biomonitoring Tool written by Elizabeth Anne Andruszkiewicz and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Marine ecosystems are threatened by anthropogenic stressors including overfishing, coastal development, pollution, and global climate change. To protect marine organisms, it is necessary to monitor their abundances and distributions over space and time. However, current monitoring methods are expensive, time consuming, and may be harmful to organisms and habitats. Capturing environmental DNA (eDNA), DNA shed from organisms into their environment, represents an alternative method for biomonitoring marine organisms. This method is less invasive and may be more cost effective, and thus could provide higher spatial and temporal resolution datasets describing marine organism distributions. \par Monitoring marine taxa by capturing eDNA in water samples eliminates the need to visually observe organisms to detect their presence. However, because organisms are not directly observed, it is important to understand the fate and transport of eDNA to properly interpret results. Many questions remain about how to relate the location of an organism to the location at which its eDNA is identified. The research described in this dissertation addresses questions about sampling design and mechanisms of eDNA decay, as well as introduces a modeling approach to compare relevant processes of eDNA fate and transport in the ocean. These contributions will help advance the field of eDNA beyond simply identifying the presence of marine organisms to providing information about the locations of organisms both in space and time. Chapter 2 examines differences in marine vertebrate communities identified by eDNA metabarcoding at varying spatial scales throughout Monterey Bay, California. Communities were compared in water sampled at different stations and sampling depths, as well as among biological triplicate samples. The study identified 92 distinct marine taxa at the 10 stations sampled and found differences in taxa identified between stations with different bottom depths, between different sampling depths within each station, and among biological replicates. Chapter 2 informs the implementation of sampling and interpretation of eDNA metabarcoding results for biomonitoring. Chapter 3 investigates the role of sunlight in eDNA decay in marine water. Mesocosms seeded with vertebrate eDNA were subject to two different sunlight exposures and then analyzed using both quantitative PCR and eDNA metabarcoding. The study found that eDNA exhibited first order decay with rate constants of approximately 0.01 1/hr and that there was no significant difference in rate constants despite the difference in sunlight exposure between the mesocosms. The results suggest that other mechanisms besides sunlight are contributing to eDNA decay and that temporal effects need to be considered when interpreting results from eDNA approaches. Chapter 4 identifies the dominant processes controlling eDNA fate and transport in the ocean by introducing a modeling framework in Monterey Bay. The framework utilizes Lagrangian particle tracking in conjunction with a numerical ocean model to simulate the transport of particles representing eDNA. Simulations were run using estimates of ocean currents over one year (2015) to vary oceanographic conditions and two settling rates and two decay rate constants were applied to vary relevant eDNA parameters. Results suggest that horizontal advection, decay, and settling have greater impacts on the displacement of eDNA in the ocean than dispersion, and that eDNA can be transported on the order of tens of kilometers after 7 days. Chapter 4 provides the first simulations of eDNA transport in the ocean and suggests that many processes need to be considered when interpreting eDNA measurements from field samples. The research documented in this dissertation represents a comprehensive approach to understanding eDNA persistence and transport in the marine environment. Results from these laboratory, field-scale, and modeling studies contribute findings to the growing field of eDNA research. Overall, the work comprises an effort to better understand how eDNA sampling events relate to the time and location of shedding of eDNA from an organism in order to more effectively use eDNA methods as biomonitoring tools in the ocean.
Download or read book Marine Algae of California written by Isabella A. Abbott and published by Stanford University Press. This book was released on 1992-08-01 with total page 856 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a complete, systematic treatment of the marine algae (seaweeds) flora of California. The 726 species treated are each illustrated by a detailed line drawing made from an actual specimen. The two authors have drawn upon their phycological research to offer a definitive representation of benthic marine algae from the Californian coast. The floristic treatment in this first paperback edition should aid accurate and speedy identification of flora due to the improved keys, descriptions, illustrations and more detailed coverage of taxa, and should enhance the reader's knowledge of Californian macro-algae.
