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 zur Erstellung und Verwaltung von Diatomeen Barcodes

Qualité de l'eau - Rapport technique relatif à la gestion des codes barres diatomées

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

Status
Published
Publication Date
11-Sep-2018
Current Stage
6060 - Definitive text made available (DAV) - Publishing
Due Date
12-Sep-2018
Completion Date
12-Sep-2018

Buy Standard

Technical report
-TP CEN/TR 17244:2019
English language
11 pages
sale 10% off
Preview
sale 10% off
Preview

e-Library read for
1 day

Standards Content (sample)

SLOVENSKI STANDARD
SIST-TP CEN/TR 17244:2019
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
SIST-TP CEN/TR 17244:2019 en

2003-01.Slovenski inštitut za standardizacijo. Razmnoževanje celote ali delov tega standarda ni dovoljeno.

---------------------- Page: 1 ----------------------
SIST-TP CEN/TR 17244:2019
---------------------- Page: 2 ----------------------
SIST-TP CEN/TR 17244:2019
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.
---------------------- Page: 3 ----------------------
SIST-TP CEN/TR 17244:2019
CEN/TR 17244:2018 (E)
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

---------------------- Page: 4 ----------------------
SIST-TP CEN/TR 17244:2019
CEN/TR 17244:2018 (E)
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.

---------------------- Page: 5 ----------------------
SIST-TP CEN/TR 17244:2019
CEN/TR 17244:2018 (E)
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.
---------------------- Page: 6 ----------------------
SIST-TP CEN/TR 17244:2019
CEN/TR 17244:2018 (E)
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
---------------------- Page: 7 ----------------------
SIST-TP CEN/TR 17244:2019
CEN/TR 17244:2018 (E)
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 familie
...

Questions, Comments and Discussion

Ask us and Technical Secretary will try to provide an answer. You can facilitate discussion about the standard in here.