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SLU-network for DNA-barcoding
2015-04-30
Maria Kahlert
Gunilla Ejdung, Åsa M Andersson, Ulrika
Stensdotter Blomberg
Enheten för miljöövervakning
Kunskapsavdelningen
Hav- och vattenmyndighet
Ola Inghe
Enheten för natur och biologisk
mångfald
Avdelningen för analys och forskning
Naturvårdsverket
Knowledge gaps for developing DNA barcoding for
environmental assessment
During the SLU workshop ’Barcoding och eDNA’ held 18/11 2014 in the
framework of the SLU ‘Temadag om smartare miljöanalysmetoder’ (Theme
day about smarter environmental analysis methods), the two present
stakeholders (The Swedish Agency for Marine and Water Management, The
Swedish Environmental Protection Agency) asked for a compiled list of all
that is required to apply and develop the new method DNA-barcoding for
environmental monitoring and assessment, to underlie resource priorities
and assist long-term strategic resource planning. With this letter, the
members of the SLU-network for DNA-barcoding have jointly compiled a
list which we think will be useful in this planning.
The SLU-network for DNA-barcoding was founded in 2014 to gather
researchers and analysts working within ecological research and/or
environmental monitoring and assessment at SLU, using or planning to use
DNA-barcoding in their work. The aim of the network is to exchange
knowledge, and explore possibilities for the large-scale use of DNAbarcoding within environmental monitoring and assessment. Maria Kahlert
from the Department of Aquatic Sciences and Assessment initiated this
network, which got funding from SLU to have workshops and seminars.
DNA-barcoding is a method that allows separating taxa within a group of
organisms by using short sequences of DNA from defined parts of the DNA.
This technique could be used in environmental monitoring as a costeffective and fast method to identify microbial organisms, such as bacteria,
fungi and algae, replacing resource demanding microscopy analyses. In
many cases, DNA based methods is the only way to retrieve species level
information e.g. for many microorganisms, larval stages, traces of fish or
other organisms in the environment or diet analyses. In addition, since the
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sensitive molecular methods require only traces of DNA in the environment,
they may be used in assessment and monitoring of rare and potentially
threatened species, or for early detection of invasive species. Also,
intraspecific genetic variation can be analyzed from environmental samples
to follow populations of specific taxa.
However, there are still many issues that have to be solved, and new
methods that have to be developed, before molecular methods may be
routinely implemented in environmental monitoring programs. Many of
these aspects are usually not regarded as ‘original research’, making funding
from research councils, such as VR or FORMAS, unlikely. We have
identified some basic needs required for an implication of DNA-barcoding
in environmental assessment and monitoring to be possible:
(i) development of high quality reference databases for organisms such as
freshwater benthic algae and phytoplankton
(ii) development of standardized and effective methods for sampling,
storing and extracting DNA from different environment such as soil, air,
water or digested material
(iii) development of downstream pipelines for data analysis and data
archiving
(i) One of the basic needs is to develop reference databases that enable
connection of barcode data to species, and to include voucher species. In
this context it is central to consider how the phylogenetic species concept
relates to the morphological one. This work needs to be done for all
organism groups, with a special emphasis on organism groups where
barcoding work just has started such as for invertebrates, phytoplankton and
benthic algae. Resources need to be allocated for researchers to find the
gaps in the references libraries and to isolate, culture and barcode the
missing species. In addition, recent results have shown that the current
morphological species concept does not necessarily overlap with the
phylogenetic species concept (based on barcoding sequences), and new
ways must be found to harmonize the efforts and to extract as much as
possible information on both the traditional monitoring methods as well as
the new ones. For many organism groups, resources should be allocated to
get a harmonized discussion about taxonomy, such as it is done currently for
fungi.
(ii, iii) The other two major fields to develop for DNA barcoding in
environmental assessment concern (ii) the methods to obtain sequence data
e.g. sampling strategies, sample handling, DNA extraction, amplification
and sequencing and (iii) the post-sequencing analysis and interpretation of
the data. There are currently many methods available, but standardized
protocols are usually not established, as it is still not clear which method
works best for a particular organism group or environmental sample.
Resources need to be allocated for testing sampling and laboratory
protocols, which include large costs on the sequencing and bioinformatic
analyses. Resources need to be allocated for researchers familiar with the
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traditional identification of the target organisms to compare the results
qualitatively and quantitatively with ones obtained from sequencing data.
Herewith, the SLU-network for DNA-barcoding is inviting interested
stakeholders for further discussion, expecting a fruitful dialogue.
Signatures
Maria Kahlert, Dept. of Aquatic Sciences and Assessment
Valerio Bartolino, Dept. of Aquatic Resources
Andrea Belgrano, Dept. of Aquatic Resources
Anna Berlin, Dept. of Forest Mycology and Plant Pathology
Johanna Boberg, Dept. of Forest Mycology and Plant Pathology
Patrik Bohman, Dept. of Aquatic Resources
Michelle Cleary, Southern Swedish Forest Research Centre
Johan Dicksved, Dept. of Animal Nutrition and Management
Stina Drakare, Dept. of Aquatic Sciences and Assessment
Lennart Edsman, Dept. of Aquatic Resources
Annika Felton, Southern Swedish Forest Research Centre
Ann-Britt Florin, Dept. of Aquatic Resources
Hanna Friberg, Dept. of Forest Mycology and Plant Pathology and Centre
for Biological Control
Björn Lindahl, Dept. of Soil and Environment
Karl Lundström, Dept. of Aquatic Resources
Kamyar Mogodiniyai Kasmaei, Dept. of Animal Nutrition and Management
Jonàs Oliva, Dept. of Forest Mycology and Plant Pathology
Åke Olson, Dept. of Forest Mycology and Plant Pathology
Stefan Palm, Dept. of Aquatic Resources
Jan Stenlid, Dept. of Forest Mycology and Plant Pathology
Malin Strand, Swedish Species Information Centre
Astrid Taylor, Dept. of Ecology
PS. SLU has furthermore just started an initiative to identify important
methods and analysis tools for a cost effective environmental monitoring
and assessment for the future. The aim is to identify stakeholder
requirements, knowledge gaps and resource needs. The project group
consists of members from all three faculties at SLU, Stina Drakare, AnnaLena Axelsson and Agneta Oskarsson, and will run for two years. DNA
barcoding is one of the so far four focus areas identified by the initiative.
Expect to get more information and invitations from SLU to further discuss
important emerging methods like DNA barcoding methods.
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