DOI: 10.5061/dryad.kb88d
title: Data from: Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

description: 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.
description: 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