The Swedish Environmental Protection Agency (EPA) and the Swedish Agency for Marine and Water Management (SwAM) invite researchers to apply for projects related to A) development of field sampling methods and techniques, sample processing and storage of environmental DNA samples, and B) generate DNA barcodes within environmental monitoring priority organism groups to identify species.
With this call the Swedish EPA and SwAM are seeking to fund research that enables better and more efficient environmental monitoring through the introduction of new DNA-based analysis technology. The size of the call is about 37 million SEK, distributed over three years (2019-2021).
The closing date for applications is September 13, 2018.
Environmental challenges in this area
Species diversity is a key component of biodiversity and the conservation of viable populations of species is an important goal in many international conventions and EU directives as well as in the Swedish environmental objective system. Monitoring of species and species groups has a great potential as indicators of environmental quality and environmental impacts of various kinds.
Today, species monitoring is very insufficient, since available surveillance methods are often very expensive. Therefore, only a fraction of relevant species has been monitored. In making tough priorities between relevance of surveillance and what is economically and practically feasible, it is the rule rather than the exception that relevant groups of species not have been monitored. For species where monitoring has been carried out, rising costs of salaries and lack of taxonomic expertise have been a growing problem.
Two molecular genetic technologies have special potential to address the problems: environmental DNA analysis (eDNA) and DNA barcoding, in combination sometimes called metabarcoding. Environmental DNA analysis is performed on DNA extracted directly from environmental samples that may contain several organisms or traces of organisms in a sample. For example, it may be water samples, bottom sediment samples, soil samples, bird pellets (castings) or stomach content.
Time-consuming procedures such as manual sorting of individuals by species and/or species identification with microscope may be more or less eliminated.
DNA barcoding involves species determination by analyzing specific gene sequences, which are used as barcodes to identify specific species.
Priorities
The call is divided in two parts and the aim is to give prerequisites for the introduction of DNA barcoding methods in environmental monitoring.
Part A.
Development of methods and techniques for field sampling, sample processing and storage of environmental DNA samples
Method development may be needed in several stages:
- Sampling strategy for sampling sites in order to collect statistically representative relevant information on existing species diversity of the sampling site.
- Method and instrument for sample collection. Collection of individual samples may also involve a sampling problem. Other problems may concern logistics, economy and risk of sample contamination.
- Routines for handling collected samples in the field and during transport to the laboratory. Problems may include the need for conservation and protection against contamination.
- Treatment and storage of samples after arrival to the laboratory and before DNA extraction.
- Preparation of samples for DNA extraction may depend on which taxonomic groups to be analyzed, or which sequences to be determined. Among other things, it is necessary to clarify whether different types of samples may require different extraction methods.
- Treatment of samples to be stored in specimen banks for later analysis. How to best store samples where DNA is not extracted to facilitate subsequent DNA analyzes?
The following sample types are prioritized: water samples, bottom sediment samples and soil samples (including litter).
Part B.
Generating DNA barcodes within environmental monitoring priority organism groups to identify species
Prioritized are projects that generate DNA reference sequences, where such are lacking or are of poor quality, for species and species groups (taxonomic or functional) that (1) are important for Swedish environmental monitoring in a broad sense, (2) where existing monitoring is inadequate or missing completely or (3) is costly and where the DNA technology has high savings potential.
Within that framework, priority is given to:
- Groups of species holding important ecosystem functions, such as phytoplankton, zooplankton, algae, benthic fauna, soil fungi, soil bacteria and soil fauna. (Heterotrophic bacteria are not prioritized in aquatic environments).
- Species with high indicator value for environmental quality.
- Endangered species, especially if they are subject to active measures.
- Early detection of invasive species.
The projects should include analysis of the various possible barcode sequences' ability to handle the degree of degradation in the environmental DNA samples and/or possible species separation problems in the relevant species groups.
Taxonomic analysis based on sequencing may be included if relevance from an environmental monitoring perspective can be justified, for example, to solve problems with taxonomic groups where different species may have completely different environmental requirements and thus different environmental indicator values.
The organisms that will form the basis of the reference barcode must be collected in places so that they represent the areas in which Swedish environmental monitoring is conducted. Generated sequences should be uploaded to relevant reference databases such as BOLD, UNITE or SILVA.
Instructions
Part A: Research projects of two to six million SEK are funded over a period of up to three years (2019-2021). The aim is to grant several projects with a combined budget of approximately 25 million SEK (including overhead costs).
Part B: Research projects of two to six million SEK are financed over two to three years. Projects including smaller taxonomic or ecological groups may be smaller and shorter. The aim is to grant several projects with a combined budget of approximately 12 million SEK (including overhead costs).
Separate application and project description shall be made for Part A and Part B as they will be individually reviewed in two separate groups. You may also apply for research grants for projects that concern only one of the parts A and B.
It is important that the relevance for the Swedish EPA or SwAM is clearly stated and described in the application.
The main applicant must hold a PhD and conduct research at universities, colleges, research institutes, or government agencies carrying out research as part of their mandate. The main applicant should be affiliated with a Swedish organization with a Swedish corporate identity number (“organisationsnummer”).
The applications are reviewed by international experts and the application should be written in English. The application is made electronically via the Swedish EPA's application portal.
Granted researches are expected to participate in the Swedish EPA's annual research conference, annual project meetings, and to allocate resources for communication with the Swedish EPA and with other stakeholders.
- For more information, see "Instructions for Applicants, Research"
Important dates
• September 13, 2018: Deadline for application
• December 2018: Funding decision
• January 2019: Projects start
How to apply
Contact information
Gunilla Ejdung, Phone: 010-698 14 20
Martin Gustafsson, Phone: 010-698 16 37
Background material
Rasmus Hovmöller, Mattias Forshage och Fredrik Ronquist: Streckkodning av den svenska floran och faunan – förutsättningar och utmaningar. PM från Naturhistoriska riksmuseet. 2017:1. (In Swedish).