SIST-TP CEN/TR 17244:2019
(Main)Water quality - Technical report for the management of diatom barcodes
Water quality - Technical report for the management of diatom barcodes
This technical report specifies the data and metadata necessary to validate the identity of a diatom barcode used for ecological assessment along with recommendations for storage of the barcode and metadata to ensure access to this information.
Wasserbeschaffenheit - Technischer Bericht zum Management von Diatomeen-Barcodes zur Bewertung des ökologischen Zustands
Qualité de l'eau - Rapport technique relatif à la gestion des codes barres Diatomées pour l'évaluation du statut écologique
Le présent rapport technique spécifie les données et les métadonnées nécessaires pour valider l’identité
d’un code‐barres Diatomées utilisé pour l’évaluation écologique ainsi que des recommandations
relatives au stockage du code‐barres et des métadonnées pour assurer l’accès à ces informations.
Kakovost vode - Tehnično poročilo o upravljanju z barkodami kremenastih alg
To tehnično poročilo določa podatke in metapodatke, ki so potrebni za potrditev identitete kremenastih alg z barkodami, skupaj s priporočili za shranjevanje barkode in metapodatkov, da se zagotovi dostop do teh informacij.
General Information
Standards Content (Sample)
SLOVENSKI STANDARD
01-julij-2019
Kakovost vode - Tehnično poročilo o upravljanju z barkodami kremenastih alg
Water quality - Technical report for the management of diatom barcodes
Wasserbeschaffenheit - Technischer Bericht zum Management von Diatomeen-
Barcodes zur Bewertung des ökologischen Zustands
Qualité de l'eau - Rapport technique relatif à la gestion des codes barres Diatomées
pour l'évaluation du statut écologique
Ta slovenski standard je istoveten z: CEN/TR 17244:2018
ICS:
13.060.70 Preiskava bioloških lastnosti Examination of biological
vode properties of water
2003-01.Slovenski inštitut za standardizacijo. Razmnoževanje celote ali delov tega standarda ni dovoljeno.
CEN/TR 17244
TECHNICAL REPORT
RAPPORT TECHNIQUE
September 2018
TECHNISCHER BERICHT
ICS 13.060.70
English Version
Water quality - Technical report for the management of
diatom barcodes
Qualité de l'eau - Rapport technique relatif à la gestion Wasserbeschaffenheit - Technischer Bericht zur
des codes barres Diatomées pour l'évaluation du statut Erstellung und Verwaltung von Diatomeen Barcodes
écologique
This Technical Report was approved by CEN on 14 May 2018. It has been drawn up by the Technical Committee CEN/TC 230.
CEN members are the national standards bodies of Austria, Belgium, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia,
Finland, Former Yugoslav Republic of Macedonia, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Latvia, Lithuania,
Luxembourg, Malta, Netherlands, Norway, Poland, Portugal, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, Switzerland,
Turkey and United Kingdom.
EUROPEAN COMMITTEE FOR STANDARDIZATION
COMITÉ EUROPÉEN DE NORMALISATION
EUROPÄISCHES KOMITEE FÜR NORMUNG
CEN-CENELEC Management Centre: Rue de la Science 23, B-1040 Brussels
© 2018 CEN All rights of exploitation in any form and by any means reserved Ref. No. CEN/TR 17244:2018 E
worldwide for CEN national Members.
Contents Page
European foreword . 3
Introduction . 4
1 Scope . 5
2 Normative references . 5
3 Terms and definitions . 5
4 Procedure. 6
4.1 DNA Harvesting . 6
4.2 Storage of barcode . 6
4.3 Storage of voucher specimens . 7
5 Associated metadata . 7
5.1 Metadata – general remarks . 7
5.2 Categies of metadata . 7
5.2.1 DNA Marker . 7
5.2.2 Culture Details . 8
5.2.3 Taxon information . 8
5.2.4 Identification . 9
5.2.5 Sampling . 9
5.2.6 Voucher . 9
Bibliography . 11
European foreword
This document (CEN/TR 17244:2018) has been prepared by Technical Committee CEN/TC 230 “Water
analysis”, the secretariat of which is held by DIN.
Attention is drawn to the possibility that some of the elements of this document may be the subject of
patent rights. CEN shall not be held responsible for identifying any or all such patent rights.
Introduction
WARNING — Persons using this technical report should be familiar with normal laboratory practice.
This European technical report does not purport to address all of the safety problems, if any, associated
with its use. It is the responsibility of the user to establish appropriate health and safety practices and
to ensure compliance with any national regulatory conditions.
Diatoms are unicellular microalgae present in all types of water bodies. They are an important
component of aquatic ecosystems and have been used widely for ecological assessment required by the
Water Framework Directive (2000/60/EC) and Urban Waste Water Treatment Directive (91/217/EEC)
in addition to other EU Directives and international agreements. The use of diatoms as indicators of
water quality is based on observations that diatom taxa have distinct preferences for particular
environmental conditions such as nutrients, organic pollution and acidity. Polluted waters will tend to
support higher proportions of those taxa whose optima correspond with the levels of the pollutant in
question. Conversely, certain species are intolerant of elevated levels of one or more pollutants, whilst
others may occur in a wide range of water qualities.
Methods using diatoms to assess water quality and ecological status based on optical microscopy have
been developed in several European countries. Methods for sampling and preparation are similar [4],
[8] leading to the development of European Standards which, in turn, facilitated the harmonization of
ecological assessment approaches [5], [6], [1]. More recently, however, molecular biology has presented
new opportunities for assessment of ecological status using diatoms (e.g. [7], [10]. Such procedures,
however, are not covered by existing standards.
A database of validated barcodes is an essential foundation of any assessment system that uses
molecular data to determine the identities of organisms. This technical report covers the steps that
should be taken if a barcode is to be correctly assigned to the appropriate taxon in a manner that can be
readily checked and authenticated by other users. These instructions will enable method developers to
ensure that they have provided all of the metadata necessary to validate the identity of a barcode and, if
followed, will ensure that reliable identifications can be made from environmental samples.
According to the precise usage to which this technical report is to be put it is essential for specifiers and
users to mutually agree on any necessary variations or optional procedural details prior to use.
All numerical values given in this technical report are approximate.
1 Scope
This technical report specifies the data and metadata necessary to validate the identity of a diatom
barcode used for ecological assessment along with recommendations for storage of the barcode and
metadata to ensure access to this information.
2 Normative references
There are no normative references in this document.
3 Terms and definitions
For the purposes of this document, the following terms and definitions apply.
ISO and IEC maintain terminological databases for use in standardization at the following addresses:
• IEC Electropedia: available at http://www.electropedia.org/
• ISO Online browsing platform: available at http://www.iso.org/obp
3.1
barcode
stretch of a DNA sequence at least 100 base pairs in length that uniquely identifies a specific taxon
3.2
base pair
pair of complementary cross-linked nucleotides that is the building block of the DNA double helix
3.3
cultivator
conservator Person responsible of the cultivation of the diatom strain
3.4
diatoms
group of unicellular algae, some of which form chains or colonies, with cell walls made of silica. They
are major contributors to primary productivity worldwide and are often used in ecological assessment
3.5
DNA marker
name of the coding or non-coding region (e.g. gene, spacer region) within the genome from which the
barcode has been amplified. The naming of the coding or non-coding regions should follow standard
scientific practice
3.6
ecological status
measure of the structure and functioning of aquatic communities
3.7
frustule
cell wall of diatoms, composed of silica and consisting of two valves linked by two or more girdle bands
3.8
habitat
specific environment in which an organism lives
3.9
isolate
population or populations of diatom cells in axenic or unialgal culture, derived from a single cell
3.10
isolator
person responsible of the isolation of the cell from which the clonal culture was established
3.11
pherogram
graphical account of the results from Sanger sequencing where each nucleotide is represented by a
single peak and the sequence of peaks correlates to the DNA sequence
3.12
primer
strand of nucleic acid that serves as starting point for DNA replication
3.13
PCR
Polymerase Chain Reaction: process used for amplification of a given region of DNA
3.14
taxa
taxonomic units, for example families, genera or species
3.15
Taxonomic Backbone
index of published taxon names which is used by databases to automatically cross-reference name
entries
3.16
valve
structural component of the diatom frustule (3.7)
3.17
voucher
physical record of a sample deposited in a collection
4 Procedure
4.1 DNA Harvesting
DNA is extracted from cultures that derive from a single algal cell but do not need to be axenic. The
culture needs to have a strain identifier given by the conservator. It is also possible to obtain barcodes
by other means (e.g. extraction of DNA from a single cell) but methods are still under development and
the difficulties of providing adequate voucher material make these methods suboptimal for establishing
barcode references. The procedure described here remains the most reliable approach. The DNA (or a
portion of it) may be stored in a biological specimen collection, e.g. an institution affiliated to the DNA
bank network.
4.2 Storage of barcode
The DNA barcode shall be stored digitally in publicly accessible databases. Examples include
EMBL/Genbank, Algaterra, Rsyst.
4.3 Storage of voucher specimens
A physical voucher of the strain from which the DNA was taken in order to produce the barcode should
be deposited in a recognized natural history collection. Duplicate of this voucher should be deposited in
a different recognized collection. The physical voucher shall include a permanently labelled microscope
slide of the cultivated strain, comprising frustules and/or valves obtained from the strain at the time of
DNA extraction. The voucher may also include loose dried material and other preparations (e.g.
scanning electron microscopy stubs) used to identify the taxon. It may also contain a slide of the original
source community.
Pictures are considered part of the voucher and should be deposited along with the voucher specimen.
The pictures should show details important for identification. Photographs should be taken from
voucher material and labelled permanently via burnt-in annotation giving the strain name.
5 Associated metadata
5.1 Metadata – general remarks
If a sequence is to be used as a normative barcode for a particular taxon it shall be accompanied by a
minimum set of metadata. This has to be stored in a digitally in publicly accessible database such as in
EMBL/Genbank, Algaterra, R-Syst. The metadata have to be linked to the barcode via a unique identifier
assigned by the database where the sequence is stored (e.g. accession numbers of EMBL/Genbank). If
strain numbers are available these should be used to establish links with other databases.
Metadata should include information, as detailed below, on the DNA marker, strain cultivation details,
taxon name, identification, sample location, voucher location and barcode authors.
5.2 Categies of metadata
5.2.1 DNA Marker
5.2.1.1 Obligatory data
— Sequencing technology
— Name of DNA marker
— Name of barcode
— Origin of DNA (whether DNA was extracted from a culture or a single cell)
— When more of the DNA marker than the barcode region has been sequenced (i.e., a longer
sequence):
— All primers used (Names and sequences (citations of first publication, if applicable). They
should be given in 5’->3’ direction.
— When only the barcode region has been sequenced:
— Forward Primer (Name and sequence (citation of first publication, if applicable) of primer at
the 5’ end). It should be given in 5’->
...
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