Suchergebnisse

This work was funded by University of Oviedo, Asturias and Spanish governments through the National Projects CGL2013-42415-R and CGL-2016-79209-R. This paper is a contribution from the Marine Observatory of Asturias (OMA) and the Research Group GRUPIN-2014-093.

The effects of the abrupt input of high quantities of dissolved inorganic nitrogen and phosphorus on prokaryotic and eukaryotic microbial plankton were investigated in an attempt to simulate the nutrient disturbances caused by eutrophication and climate change. Two nutrient levels were created through the addition of different quantities of dissolved nutrients in a mesocosm experiment. During the developed blooms, compositional differences were found within bacteria and microbial eukaryotes, and communities progressed towards species of faster metabolisms. Regarding the different nutrient concentrations, different microbial species were associated with each nutrient treatment and community changes spanned from the phylum to the operational taxonomic unit (OTU) level. Network analyses revealed important differences in the biotic connections developed: more competitive relationships were established in the more intense nutrient disturbance and networks of contrasting complexity were formed around species of different ecological strategies. This work highlights that sudden disturbances in water column chemistry lead to the development of entirely different microbial food webs with distinct ecological characteristics. ; This work was funded by the European Union and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) – ARISTEIA II (HYPOXIA project, No 4705), and by King Abdullah University of Science and Technology (KAUST) through baseline funding to DD. We are grateful to the participants of the mesocosm experiment for their significant help during experimental setup and sampling: S. Diliberto, C. Frangoulis, A. Geropoulos, V. Kalogeropoulou, M. Kanellopoulou, M. Moraitis, and Tsikopoulou I. Special thanks are attributed to E. Dafnomili, M. Kagiorgi and S. Zivanovic for assistance with dissolved nutrients analyses and G. Piperakis for inspiring technical assistance. J.B. Kristoffersen and C. Pavloudi are greatly acknowledged for valuable advising during molecular analyses.This work was funded by the European Union and Greek national funds through the Operational Program "Education and Lifelong Learning" of the National Strategic Reference Framework (NSRF) – ARISTEIA II (HYPOXIA project, No 5381), and by King Abdullah University of Science and Technology (KAUST) through baseline funding to DD. The authors declare no conflict of interest. All authors have approved the final submitted manuscript.

AbstractThe German National Reference Centre for Authentic Food (NRZ-Authent) and the competent German food control authorities of the federal states cooperated within the framework of the 10th joint Europol INTERPOL operation OPSON (OPSON X) in the detection of adulterated meat products. A total of 63 meat product samples were collected and analysed by the authorities using standard analytical procedures and subjected to a recently published 16S rDNA metabarcoding analysis. The sequence reads were analysed using 3 bioinformatics data processing strategies. The study aimed to gain additional data on the test samples regarding the authenticity of the declared species and to validate the 16S rDNA metabarcoding method with representative samples. The method was tested not only on 63 test samples, but also on 5 commercial samples from 2 interlaboratory comparison studies and 9 mock mixtures in parallel. The 16S rDNA metabarcoding method was able to detect species that were not target species of the used standard analytical methods, but failed, as shown previously, to detect fallow deer. Otherwise, the qualitative results of the 16S rDNA metabarcoding method were very similar to those of the methods currently in use by the German food control laboratories. Thus, the method has great potential to be used as a screening method for the authentication of mammal and poultry species in meat products.

The study of ecosystem diversity is being transformed by high throughput sequencing technology that allows an unparalleled depth of sampling of DNA barcode sequences. The opportunities are great at this fascinating interface of pathology, ecology, taxonomy and molecular biology but there are pitfalls. It is important to consider the potential for bias at all steps in the process from sampling through to data analysis. Increasingly Phytophthora diversity is being examined by metabarcoding of the PCR amplified rDNA ITS regions from soil, water or plant sample DNA. We have applied baiting and isolation, cloning and Sanger sequencing and Illumina MiSeq analysis to a time-series of filtered water samples from several Scottish streams within a UK-wide sampling network. These data, the literature and other presentations in this session will be explored in a critical analysis of the field. A specific focus will be placed on exploring the range of species and their boundaries, the potential for species quantification and possible benefits of the technology for plant health legislation.

Abstract
Background
Fungicides are frequently used in agriculture and can enter freshwater ecosystems through multiple pathways. The negative impacts of fungicides on microorganisms, fungi in particular, and their functions such as leaf decomposition have been repeatedly shown. In our previous microcosm experiment with three consecutive cycles of fungicide exposure and colonisation of leaf substrate, we found clear functional changes, but no differences in fungal community structure could be detected using morphological identification by analysing the spores of aquatic hyphomycetes. In this study, we examined the effects on fungal and bacterial community composition in detail using ITS and 16S metabarcoding and comparing the results to morphologically assessed community composition.

Results
While we found fewer species with metabarcoding than with morphological identification, metabarcoding also enabled the identification of several fungal species that were otherwise unidentifiable morphologically. Moreover, by distinguishing individual amplicon sequence variants (ASVs) metabarcoding provided greater taxonomic resolution. In line with the morphological results, metabarcoding neither revealed effects of fungicides on the aquatic hyphomycetes nor on the total fungal or bacterial community composition. However, several ASVs responded significantly to fungicides, demonstrating variable tolerances within species.

Conclusions
Overall, the absence of detectable effects of fungicides on the community structure despite clear functional effects, suggests a complex relationship between community structure and the ecosystem function of leaf decomposition.

This article belongs to the Special Issue Role of Human Interventions in Spread of Soilborne Forest Pathogens and Methods for Mitigation. ; Disease outbreaks caused by introduced Phytophthora species have been increasing in British forests and woodlands in recent years. A better knowledge of the Phytophthora communities already present in the UK is of great importance when developing management and mitigation strategies for these diseases. To do this, soils were sampled in "disturbed" sites, meaning sites frequently visited by the public, with recent and new plantings or soil disturbances versus more "natural" forest and woodland sites with little disturbance or management. Phytophthora diversity was assessed using high-throughput Illumina sequencing targeting the widely accepted barcoding Internal Transcribed Spacer 1 (ITS1) region of rRNA and comparing it with the mitochondrial cytochrome c oxidase I (COI) gene. Isolation of Phytophthora was run in parallel. Nothophytophthora spp. and Phytophthora spp. were detected in 79 and 41 of the 132 locations of the 14 studied sites when using ITS or COI, respectively. A total of 20 Phytophthora amplicon sequence variants (ASVs) were assigned to known Phytophthora species from eight clades (1a, 2, 2b, 3a, 5, 6b, 7a, 8b, 8c, 8d, 10a, and 10b) and 12 ASVs from six clades (1a, 2c, 3a, 3b, 6b, 7a, 8b, 8c, and 8d) when using ITS or COI, respectively. Only at two locations were the results in agreement for ITS, COI, and isolation. Additionally, 21 and 17 unknown Phytophthora phylotypes were detected using the ITS and COI, respectively. Several Phytophthora spp. within clades 7 and 8, including very important forest pathogens such as P. austrocedri and P. ramorum, were identified and found more frequently at "disturbed" sites. Additionally, eight ASVs identified as Nothophytophthora spp. were detected representing the first report of species within this new genus in Britain. Only three species not known to be present in Britain (P. castaneae, P. capsici, and P. fallax) were detected with the ITS primers and not with COI. To confirm the presence of these or any potential new Phytophthora species, sites should be re-sampled for confirmation. Additionally, there is a need to confirm if these species are a threat to British trees and try to establish any eradication measures required to mitigate Phytophthora spread in Britain. ; This work has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 635646, POnTE (Pest Organisms Threatening Europe).

Este artículo contiene 16 páginas, 5 figuras. ; DNA metabarcoding is broadly used in biodiversity studies encompassing a wide range of organisms. Erroneous amplicons, generated during amplification and sequencing procedures, constitute one of the major sources of concern for the interpretation of metabarcoding results. Several denoising programs have been implemented to detect and eliminate these errors. However, almost all denoising software currently available has been designed to process non-coding ribosomal sequences, most notably prokaryotic 16S rDNA. The growing number of metabarcoding studies using coding markers such as COI or RuBisCO demands a re-assessment and calibration of denoising algorithms. Here we present DnoisE, the first denoising program designed to detect erroneous reads and merge them with the correct ones using information from the natural variability (entropy) associated to each codon position in coding barcodes. We have developed an open-source software using a modified version of the UNOISE algorithm. DnoisE implements different merging procedures as options, and can incorporate codon entropy information either retrieved from the data or supplied by the user. In addition, the algorithm of DnoisE is parallelizable, greatly reducing runtimes on computer clusters. Our program also allows different input file formats, so it can be readily incorporated into existing metabarcoding pipelines. ; This research was funded by the projects PopCOmics (CTM2017-88080, MCIN/AEI/10.13039/ 501100011033 and ``ERDF A way of making Europe'', EU), MARGECH (PID2020- 118550RB, MCIN/AEI/10.13039/501100011033), and BigPark (OAPN, 2462/2017) from the Spanish Government. The publication charges for this article have been funded by a grant from the publication fund of UiT The Arctic University of Norway. ; Peer reviewed

Cover -- Half Title -- Series Information -- Title Page -- Copyright Page -- Table of Contents -- Acknowledgements -- Contributors -- Part I Environment Management and Monitoring -- 1 Environment Studies and Climate Change: a Bibliometric Analysis -- 1.1 Introduction: Environment and Climate Change -- 1.2 Research Methodology -- 1.4 Bibliometric Analysis -- 1.4.1 Author's Keywords Co-occurrence Analysis -- 1.4.2 Citation Analysis by Country (on the Basis of First 2000 Documents) -- 1.6 Conclusion -- References -- 2 Environmental Implications of Persistent Organic Pollutants (POPs) -- 2.1 Introduction -- 2.2 Discovery and Prohibition of Persistent Organic Pollutants -- 2.3 Types and Classification of Intentional and Unintentional Persistent Organic Pollutants -- 2.4 Properties and Sources of Intentionally Produced POPs -- 2.5 Properties and Sources of Unintentionally Produced POPs -- 2.6 Risk Associated with Intentionally and Unintentionally Produced POPs -- 2.7 Transport and Fate of POPs -- 2.8 Impacts of Intentionally and Unintentionally Produced POPs on Climate Change -- 2.8.1 Consequences of Elevated Temperature for the Dispersal of POPs -- 2.8.2 Role of Rainfall in the Dispersal of POPs -- 2.8.3 Sea-level and Dispersal of POPs -- 2.8.4 Role of CO2 Rise in the Dispersal of POPs -- 2.9 Conclusion -- References -- 3 DNA Barcoding and Metabarcoding: A Potential Tool for Environmental Biodiversity Monitoring -- 3.1 Introduction -- 3.2 Methods for Biodiversity Monitoring -- 3.3 DNA Barcoding -- 3.4 Metabarcoding -- 3.5 Estimating Biodiversity by Metabarcoding -- 3.5.1 Applications of DNA Barcoding and Metabarcoding -- 3.5.2 Limitations of DNA Barcoding and Metabarcoding -- 3.6 Conclusion -- References -- 4 Effect of Flow Alteration on River Ecology: State of the Art -- 4.1 Introduction -- 4.2 Salient Features of Natural Flow Regime in Rivers.

Mit dem Projekt "eDNA-basierte Verfahren in der behördlichen Praxis" soll eine Flächenstudie an Fließgewässern durchgeführt werden, um das Potenzial genetischer Methoden (DNA-Metabarcoding) zur Beurteilung des ökologischen Zustands für die in der Bewertungspraxis der EG-Wasserrahmenrichtlinie genutzten (verbindlichen) Biologischen Qualitätselemente (BQEs) zu testen. Probenahme- und Laborprotokolle sollen für die drei BQEs Makrozoobenthos, Diatomeen als 'Proxies' für Phytobenthos (im Folgenden aber weiter als Diatomeen bezeichnet) und Fische bis zur Anwendungsreife im behördlichen Alltag entwickelt werden. Darüber hinaus soll geprüft werden, inwiefern neue Informationen über Organismen aus den genetischen Daten abgeleitet werden können, die genauer über den Erfolg von Renaturierungsmaßnahmen informieren und zusätzliche Informationen zur Kausalanalyse des Gewässerzustandes liefern. Die Projektziele sind: 1) Die Validierung von DNA-Metabarcoding als Methode zur Beurteilung des ökologischen Zustands von Fließgewässern anhand einer großen Anzahl von Probestellen der vier häufigsten Fließgewässertypen und drei BQEs (Makrozoobenthos, Diatomeen, Fische) über einen Gradienten von Zustandsklassen. 2) Das Ableiten von Korrekturfaktoren, um DNA-basierte Methoden in die vorhandenen Bewertungssysteme integrieren zu können (Plausibilisierung). 3) Die Prüfung der Eignung von DNA-Metabarcoding für den Einsatz in der behördlichen Praxis inkl. Kosten-Nutzen-Bilanzierung im Vergleich zu konventionellen Bewertungsansätzen. 4) Das Entwickeln neuer Indikatoren, um biologische Prozesse nach Renaturierungen umfassender und aussagekräftiger zu beurteilen (Einbezug weiterer BQEs, kryptischer Arten etc.) und die Kausalanalyse der Daten zum ökologischen Zustand zu unterstützen.

Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systems ; info:eu-repo/semantics/publishedVersion

Knowledge on diet composition of a species is an important step to unveil its ecology and guide conservation actions. This is especially important for species that inhabit remote areas within biodiversity hotspots, with little information about their ecological roles. The emblematic giant wall gecko of Cabo Verde, Tarentola gigas, is restricted to the uninhabited Branco and Raso islets, and presents two subspecies. It is classified as Endangered, and locally Extinct on Santa Luzia Island ; however, little information is known about its diet and behaviour. In this study, we identified the main plant, arthropods, and vertebrates consumed by both gecko subspecies using next generation sequencing (NGS) (metabarcoding of faecal pellets), and compared them with the species known to occur on Santa Luzia. Results showed that plants have a significant role as diet items and identified vertebrate and invertebrate taxa with higher taxonomic resolution than traditional methods. With this study, we now have data on the diet of both subspecies for evaluating the reintroduction of this threatened gecko on Santa Luzia as potentially successful, considering the generalist character of both populations. The information revealed by these ecological networks is important for the development of conservation plans by governmental authorities, and reinforces the essential and commonly neglected role of reptiles on island systems.