10.5061/DRYAD.KB88D
Zimmermann, Jonas
University of Giessen
Freie Universität Berlin
Glöckner, Gernot
Leibniz Institute of Freshwater Ecology and Inland Fisheries
University of Cologne
Jahn, Regine
Freie Universität Berlin
Enke, Neela
Freie Universität Berlin
Gemeinholzer, Birgit
University of Giessen
Data from: Metabarcoding vs. morphological identification to assess diatom
diversity in environmental studies
Dryad
dataset
2014
DNA-based Species Identification
Environmental DNA Barcoding
Recent
Next Generation Sequencing
Water Monitoring
2014-10-03T15:28:38Z
2014-10-03T15:28:38Z
en
https://doi.org/10.1111/1755-0998.12336
391632114 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Diatoms are frequently used for water quality assessments; however,
identification to species level is difficult, time-consuming and needs
in-depth knowledge of the organisms under investigation, as nonhomoplastic
species-specific morphological characters are scarce. We here investigate
how identification methods based on DNA (metabarcoding using NGS
platforms) perform in comparison to morphological diatom identification
and propose a workflow to optimize diatom fresh water quality assessments.
Diatom diversity at seven different sites along the course of the river
system Odra and Lusatian Neisse from the source to the mouth is analysed
with DNA and morphological methods, which are compared. The NGS technology
almost always leads to a higher number of identified taxa (270 via NGS vs.
103 by light microscopy LM), whose presence could subsequently be verified
by LM. The sequence-based approach allows for a much more graduated
insight into the taxonomic diversity of the environmental samples. Taxa
retrieval varies considerably throughout the river system, depending on
species occurrences and the taxonomic depth of the reference databases.
Mostly rare taxa from oligotrophic parts of the river systems are less
well represented in the reference database used. A workflow for DNA-based
NGS diatom identification is presented. 28 000 diatom sequences were
evaluated. Our findings provide evidence that metabarcoding of diatoms via
NGS sequencing of the V4 region (18S) has a great potential for water
quality assessments and could complement and maybe even improve the
identification via light microscopy.
Environmental barcoding Lusatian Neisse/Odra
RiverHWFN2LX01.sffRL6.1AmphoraTreeThis .mts file was generated in MEGA 5
and may be opened in MEGA 5. To open in MEGA 6, export the tree to a .nwk
file in MEGA 5 and open the .nwk file in MEGA
6.RL6.1_AmphNCBI_20130419.mtsRL6.1CocconeisTreeThis .mts file was
generated in MEGA 5 and may be opened in MEGA 5. To open in MEGA 6, export
the tree to a .nwk file in MEGA 5 and open the .nwk file in MEGA
6.RL6.1_CoccoNCBI_20130423.mtsRL6.1_EncyonemaTreeThis .mts file was
generated in MEGA 5 and may be opened in MEGA 5. To open in MEGA 6, export
the tree to a .nwk file in MEGA 5 and open the .nwk file in MEGA
6.RL6.1_EncyoNCBI_20130423.mtsRL6.1_EolimnaTreeThis .mts file was
generated in MEGA 5 and may be opened in MEGA 5. To open in MEGA 6, export
the tree to a .nwk file in MEGA 5 and open the .nwk file in MEGA
6.RL6.1_EolimnaNCBI_20130423.mtsRL6.1_FragilariaTreeThis .mts file was
generated in MEGA 5 and may be opened in MEGA 5. To open in MEGA 6, export
the tree to a .nwk file in MEGA 5 and open the .nwk file in MEGA
6.RL6.1_FragiNCBI_20130418.mtsRL6.1_NaviculaTreeThis .mts file was
generated in MEGA 5 and may be opened in MEGA 5. To open in MEGA 6, export
the tree to a .nwk file in MEGA 5 and open the .nwk file in MEGA
6.RL6.1_NaviNCBI_20130420.mtsRL6.1_NitzschiaTreeThis .mts file was
generated in MEGA 5 and may be opened in MEGA 5. To open in MEGA 6, export
the tree to a .nwk file in MEGA 5 and open the .nwk file in MEGA
6.RL6.1_NitzNCBI_20130422.mtsRL6.1_PlanothidiumAchnanthidiumTreeThis .mts
file was generated in MEGA 5 and may be opened in MEGA 5. To open in MEGA
6, export the tree to a .nwk file in MEGA 5 and open the .nwk file in MEGA
6.RL6.1_thidiumNCBI_20130417.mts
Central Europe