While the research on environmental DNA and other genetic tools to support aquatic bioassessment progresses rapidly, few of the methods find entry in regulatory biomonitoring. To provide latest information about DNA-based aquatic bioassessment and monitoring to national stakeholders involved especially in the national implementation of European Directives and to assess where end-users from environmental agencies and offices see main challenges at national level, a set of national workshops will be held in parallel and the national languages to facilitate the dialogue just after the conference, on the 12th March 2021.

EnvMetagen, being a long-term partner of DNAqua-net has volunteered to organize this event. You can fin the program and the link to register (deadline March 9th) here: Stakeholder_workshop eDNA Portugal_12032021

Join us!! Let’s contribute to improve biomonitoring of aquatic ecosystems.

For this 10th edition, under the theme of Metabarcoding and Metagenomics, we are going virtual!

The event will take place from 9-11th December 2020, on a dedicated online platform for streaming of the presentations and networking between participants. Abstracts for oral presentations and posters are accepted until October 27th.

Keynote speakers: Mike Schwartz, National Genomics Center for Wildlife and Fish Conservation, USA ; Agnès Bouchez, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, France and Tyler Kartzinel, Brown University, USA.

More information on this page, that will be updated frequently.

METABARCODING WITH MinION: SPEEDING UP THE DETECTION OF INVASIVE AQUATIC SPECIES USING ENVIRONMENTAL DNA AND NANOPORE SEQUENCING

Bastian Egeter (CIBIO-InBIO/UP) | July 17, 2020 | 15h30 | CIBIO-InBIO’s – Online, on Zoom

Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and to substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. We extracted, amplified and sequenced eDNA with a turnaround of 3.5 days. The majority of processed reads were ≥ 99 % identical to reference sequences. There were no taxa detected other than those known to occur. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples. The approach can be easily adapted for other metabarcoding applications, such as biodiversity assessment, ecosystem health assessment and diet studies.

WEBINAR “COMPANIES TOGETHER BY NATURE: ACT4NATURE PORTUGAL”

Pedro Beja (CIBIO-InBIO/UP) | May 22, 2020 | 16h00 | Online, BCSD event

Online Talks about Sustainability is an event promoted by the Business Council for Sustainable Development (BCSD Portugal).

This week, CIBIO’s scientific vice-coordinator, Pedro Beja, will be one of the speakers in a webinar entitled “Companies together by nature: act4nature Portugal”.

The following topics will be addressed in this online session:
– The role of companies in nature protection;
– Presentation of the act4nature Portugal initiative, a joint commitment to the promotion and conservation of biodiversity;
– Clarification session about the project and invitation to companies to participate in this initiative.

To move forward on this idea, we have joined forces with our partners. This workshop, jointly organized by EnvMetaGen, CIBIO-InBIO, PORBIOTA, LifeWatch ERIC, and DNAqua-Net is a first brainstorming between the key research groups that in the national LifeWatch ERIC nodes are active on genomic approaches to biodiversity assessment, understanding, monitoring and preservation. Overall, the meeting aims to explore how LifeWatch ERIC can integrate online bioinformatics pipelines in its Virtual Research Environment, which can then be used by the wider scientific community for research and applications in the fields of biodiversity survey and environmental biomonitoring.

The event takes place from February 26-28 at CIBIO-InBIO facilities in Vairão. It can be attended by invitation only.

ADVANCING METABARCODING TECHNIQUES FOR THE STUDY OF TROPHIC INTERACTIONS AND ECOSYSTEM SERVICES IN SMALL VERTEBRATES

Vanessa Mata (CIBIO-InBIO/UP) | February 7, 2020 | 14h45 | CIBIO-InBIO’s Auditorium, Campus de Vairão, Portugal

Small insectivorous vertebrates can deliver important ecosystem services such as pest control, thereby reducing the need of agrochemical inputs. The flow, stability and resilience of such services are critically dependent on the trophic networks between these animals and their prey, which are presently poorly understood. Metabarcoding tools can offer unprecedented detail in the diet of small insectivorous vertebrates, providing key understanding on their role in the provision of ecosystem services. However, the application of these techniques is still in its infancy, and the impact of their technical caveats and limitations on the estimate of trophic interactions still needs to be fully understood. The goal of this work is to advance the use of metabarcoding techniques in the study of species interactions, thereby enhancing its applicability in the management of complex landscapes. Specifically, it aims at: i) understanding the impacts of technical and biological replication on metabarcoding dietary analysis; ii) testing the use of multiple overlapping markers in dietary analysis, and define criteria for integrating them; iii) assessing the power of taxonomically resolved dietary data to reveal subtle intraspecific variations in predator-prey relationships; and iv) evaluating species’ roles in sustaining pest regulation services in a multifunctional landscape. The results stress that maximizing biological replication is critical in dietary metabarcoding studies and that the integration of multi-marker data provides far more detailed dietary information than any single marker approach. Moreover, metabarcoding proved to be a powerful tool, capable of detecting subtle intra- and inter-specific variations. The combined use of metabarcoding with ecological network analysis further allowed the description of the first predator-pest interaction network of bats and insect agricultural pests, along with the identification of bat species that could be favoured to intensify the control of pests. Overall, this work underlined the value of metabarcoding to unravel the functional role of small vertebrates in multifunctional landscapes, while providing guidance on best practice to minimise the potential caveats and limitations of this technique.

USING METABARCODING TO STUDY THE DIET OF A GENERALIST PASSERINE: THE BLACK WHEATEAR

Luis Pascoal da Silva (CIBIO-InBIO) | November 15, 2019 | XXIV Congreso Español & VII Ibérico de Ornitología, Cadiz, Spain

Metabarcoding studies are now common in ecology and dietary studies are no exception. Metabarcoding has been used to study the diet of an incredible range of animals and even the diet of carnivorous plants, yet incredibly few focuses on passerines. Among other advantages, metabarcoding allows an unprecedent level of taxonomic resolution of ingested items. Nonetheless, this technique has many technical caveats and biases, which are still not thoroughly assessed. The aims of this work were not only to describe in detail the diet of black wheatears (Oenanthe leucura) in Portugal, but also to evaluate the advantages and pitfalls of using metabarcoding in the study of generalist bird diets. In this study we used genetic identification of 115 bird droppings with 4 molecular markers. The method allowed the description of the diet with an unpreceded detail, detecting 552 different taxa. However, there were several problems associated with the technique, namely the bias of some molecular primers towards some taxonomic groups and the detection of secondary predation. In order to avoid some of the common problems of the methodology, we recommend the use of multiple molecular primers when targeting super-diverse taxonomic prey groups and to combine the information of all the primers used in a single dataset. In the case of the black wheatear, we found its diet to be extremely wide, with the presence of reptiles, numerous orders of invertebrates and several plant species. The animal component of the Black wheatear diet was dominated by Hymenoptera, mainly ants, while fruit ingestion was also very common, especially of ruderal plants. Our results also revealed the existence of dietary differences between males and females, with males having a more diverse diet, and females preying more often on ants than males. Metabarcoding proved to be a very powerful tool in providing a better and more detailed understanding of birds? diet. Nevertheless, careful planning according to the goals and subject of the study is needed when designing laboratory procedures and analysis of metabarcoding data.

IBI – InBIO BARCODING INITIATIVE: DNA BARCODING PORTUGUESE TERRESTRIAL INVERTEBRATE BIODIVERSITY

Sónia Ferreira (CIBIO-InBIO) | November 5, 2019 | XI Congreso Nacional de Entomología Aplicada, Madrid, Spain

DNA barcoding is an essential tool for biodiversity monitoring and conservation studies. However, its applicability is hindered by the lack of comprehensive reference collections, particularly of invertebrates that are underrepresented in reference databases. In the Northwest of the Mediterranean Basin biodiversity hotspot, Portugal holds a unique and diverse fauna. Nevertheless, the vast majority of species remains  understudied and underrepresented in DNA barcoding databases. InBIO Barcoding Initiative aims to fill the gap regarding Portuguese terrestrial invertebrate taxa. By combining field work and networking with taxonomists and ecologists, more than 7,000 specimens were already collected, and over 5,000 sequenced, covering over 150 families of insects from more than 20 orders. During the development of the IBI reference collection of DNA sequences, many relevant findings on the Portuguese fauna were made. For several groups, a reasonable representation has already been achieved. The state of the art of Dermaptera, Hemiptera, Lepidoptera, Mantodea, Mecoptera, Phasmatodea, Odonata, Orthoptera and Rhaphidioptera orders will be presented. Major challenges are the hyperdiverse orders such as Coleoptera, Diptera and Hymenoptera, which represent an enormous part of the invertebrate diversity and have remarkable ecological relevance but are poorly studied in Portugal. For these groups our focus is the establishment and strengthening of collaborations with taxonomists, and the  intensification of the use of sampling techniques that target these taxonomical groups. DNA barcodes of Portuguese invertebrates facilitated the correct identification of enigmatic specimens, namely undocumented species in the region (indigenous and exotic), pinpointed the existence of undescribed species and allowed linking males and females of sexually dimorphic species. Cryptic diversity was found in several insect groups. The use of High-throughput Sequencing to produce the DNA barcodes also allowed tackling challenges posed by the existence of nuclear copies. Overall, IBI is expected to become a fundamental tool for biodiversity monitoring in Portugal.

BARCODING BIODIVERSITY: FROM SPECIES DETECTION TO FRESHWATER BIOMONITORING USING eDNA METABARCODING

Joana Paupério (CIBIO-InBIO, Portugal) | October 28, 2019 | XXIII Congreso Sociedad Mesoamericana para la Biología y la Conservación, Antigua, Guatemala

Monitoring biodiversity and understanding the drivers of change at local, regional and global scales requires detailed information on the diversity, composition and structure of biological communities, as well as on species interactions. However, for many groups and contexts, this information is still scarce due to the high biological diversity and the limits on taxonomic expertise. High throughput DNA sequencing is boosting the ability to address these issues, by allowing the identification of species occurring in a given area, through a simple and inexpensive approach. Here, we showcase the application of high throughput DNA sequencing to document biodiversity in Portugal, and the use of environmental DNA metabarcoding techniques for understanding the structure and interactions within biological communities and developing biomonitoring programs. Biodiversity surveys have been conducted to build a DNA barcode reference collection – the InBIO Barcoding Initiative, that has been mainly focusing on invertebrate taxa. Until now, over 2000 species have been inventoried and are already barcoded. Sequenced specimens are kept as vouchers for future reference, and DNA sequences are made freely available on the Barcode of Life Data system (http://v4.boldsystems.org/). This reference library holds already good representation of some groups and allowed unravelling cryptic diversity. Based on this reference, we are using metabarcoding to analyse environmental samples, including water and bulk samples, for species detection and to understand the response of communities to land use change and anthropogenic drivers. Studies of trophic interactions using these approaches are also helping clarifying the role of small mammal species in aquatic and terrestrial food chains. Moreover, these studies are directly supporting the development of freshwater biomonitoring methods based on DNA metabarcoding. Overall, we highlight the value of eDNA metabarcoding for biomonitoring.

LINKING BIODIVERSITY TO ECOSYSTEM SERVICES: THE SMALL MAMMAL COMMUNITY OF NE PORTUGAL AGROECOSYSTEMS

Joana Paupério (CIBIO-InBIO) | September 27, 2019 | 8th European Congress of Mammalogy, Warsaw, Poland

The spread and intensification of agriculture are recognised as important global threats to biodiversity, and thus to the maintenance of ecosystem functions and services. Biological pest management is one of the main ecosystem services often supported by traditional agroecosystems holding high levels of biodiversity. However, there is still limited understanding on how biodiversity levels actually relate with biological control, particularly in the case of small mammal species embedded in diverse communities facing agricultural intensification. Here we present part of the results of an ongoing research project (AGRIVOLE) that aims to unveil the response of small mammal communities to agroecosystem structure and agricultural practices, and to evaluate how such responses may affect either the potential for pest outbreaks or the persistence of species of conservation concern. Based on over 1000 barn owl pellets collected in 35 sites spatially distributed across NE Portugal, and detailed land-cover maps within 1.5 Km buffers centred in each collection site, we analyse the spatial pattern of small mammals’ community and its relation to landscape variables describing agroecosystem structure and agriculture intensification. Specifically, we use generalized linear models to test the general hypothesis that lower diversities and higher abundance of potential pests should be associated to more intensive agricultural landscapes. Overall, we expect that our results will provide useful first insights on links between small mammal diversity, and their role in agroecosystems under agricultural intensification, thereby contributing to foster sustainable agricultural management linking pest control to biodiversity conservation.