Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

Zimmermann, Jonas; Jahn, Regine; Gemeinholzer, Birgit

doi:10.1007/s13127-011-0050-6

Cited by 245 publications

(238 citation statements)

References 109 publications

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“…ribosomal, mitochondrial and chloroplast markers (e.g. 18S rRNA, cox1 and rbcL) (Evans et al 2007;Medinger et al 2010;Theriot et al 2010;Hamsher et al 2011;Zimmermann et al 2011;Epp et al 2012;Kermarrec et al 2013;StoofLeichsenring et al 2014). In our study, a short and variable sequence of 76 bp of the chloroplast rbcL gene (rbcL_76 amplicon) was used because of its specificity to the amplification of diatom DNA from sedimentary records, and especially ancient sedimentary DNA.…”

Section: Discussionmentioning

confidence: 99%

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

et al. 2016

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The Arctic treeline ecotone is characterised by a steep vegetation gradient from arctic tundra to northern taiga forests, which is thought to influence the water chemistry of thermokarst lakes in this region. Environmentally sensitive diatoms respond to such ecological changes in terms of variation in diatom diversity and richness, which so far has only been documented by microscopic surveys. We applied next-generation sequencing to analyse the diatom composition of lake sediment DNA extracted from 32 lakes across the treeline in the Khatanga region, Siberia, using a short fragment of the rbcL chloroplast gene as a genetic barcode. We compared diatom richness and diversity obtained from the genetic approach with diatom counts from traditional microscopic analysis. Both datasets were employed to investigate diversity and relationships with environmental variables, using ordination methods. After effective filtering of the raw data, the two methods gave similar results for diatom richness and composition at the genus level (DNA 12 taxa; morphology 19 taxa), even though there was a much higher absolute number of sequences obtained per genetic sample (median 50,278), compared with microscopic counts (median 426). Dissolved organic carbon explained the highest percentage of variance in both datasets (14.2 % DNA; 18.7 % morphology), reflecting the compositional turnover of diatom assemblages along the tundra-taiga transition. Differences between the two approaches are mostly a consequence of the filtering process of genetic data and limitations of genetic references in the database, which restricted the determination of genetically identified sequence types to the genus level. The morphological approach, however, allowed identifications mostly to species level, which permits better ecological interpretation of the diatom data. Nevertheless, because of a rapidly increasing reference database, the genetic approach with sediment DNA will, in the future, enable reliable Electronic supplementary material The online version of this article (doi:10.1007/s10933-016-9926-y) contains supplementary material, which is available to authorized users. 123J Paleolimnol DOI 10.1007/s10933-016-9926-y investigations of diatom composition from lake sediments that will have potential applications in both paleoecology and environmental monitoring.

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Section: Discussionmentioning

confidence: 99%

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

et al. 2016

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“…Although this review has focused on the limitations of approaches based purely on composition, future approaches will need to consider composition and new technologies such as DNA barcoding, which holds great promise (Mann et al, 2010;Zimmermann et al, 2011;Kermarrec et al, 2013) as a means of collecting basic information on composition with greater precision and lower cost than was hitherto the case. We should, however, be wary of those (Baird & Hajibabaei, 2012) who would bypass conventional taxonomy altogether.…”

Section: Summary: What Needs To Be Donementioning

confidence: 99%

Data rich, information poor? Phytobenthos assessment and the Water Framework Directive

Kelly¹

2013

European Journal of Phycology

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The Water Framework Directive (WFD) provides the legal basis for water management in the European Union (EU). Twelve years after it was passed, all but five EU Member States had phytobenthos assessment methods for rivers, whilst nine had methods for lakes. Most are based on diatoms, although a few are supplemented by evaluations of non-diatoms and some include macroalgae as part of parallel macrophyte assessments. Norway is the exception, with assessment based on non-diatom algae alone. Over half of all states have methods based wholly or partly on weighted average metrics developed before the onset of the WFD, with nine choosing the Indice de Polluosensibilité Specifique. Such metrics generally have high correlations with the predominant nutrient or organic pollution gradient and, as such, represent pragmatic solutions to ecological status assessment. However, their widespread use raises questions about what, exactly, 'ecological status' means. Strong relationships with chemical pressure gradients may be a mixed blessing as pressure gradients are often composed of several intercorrelated variables, making it difficult to disentangle correlation and causation in the absence of ecophysiological studies of individual species. Moreover, the focus on strong relationships with chemical gradients means that most phytobenthos metrics describe the scale of hazard at a site rather than the risk posed to other trophic levels and to ecosystem services. This first generation of phytobenthos assessment tools may be inadequate when catchment managers need guidance on remediation strategies for particular water bodies. A second generation of assessment tools, focused on the fitness of the phytobenthos as part of aquatic ecosystems, rather than just as indicators of chemical conditions, is needed if the goal of good ecological status around Europe is to be achieved.

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“…DNA barcodes) for species discrimination in diatoms (Evans et al 2007;Hamsher et al 2011;MacGillivary and Kaczmarska 2011;Zimmermann et al 2011). Working with environmental DNA, which is a mixture of genomic DNA from various organisms, ribosomal and mitochondrial markers with rather universal primer binding sites likely amplify non-specific DNA from related, or even distinct, taxonomic groups.…”

Section: Introductionmentioning

confidence: 99%

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

et al. 2014

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Diatom diversity in lakes of northwest Yakutia (Siberia) was investigated by microscopic and genetic analysis of surface and cored lake sediments, to evaluate the use of sedimentary DNA for paleolimnological diatom studies and to identify obscure genetic diversity that cannot be detected by microscopic methods. Two short (76 and 73 bp) and one longer (577 bp) fragments of the ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) gene, encoding the large subunit of the rbcL, were used as genetic markers. Diverse morphological assemblages of diatoms, dominated by small benthic fragilarioid taxa, were retrieved from the sediments of each lake. These minute fragilarioid taxa were examined by scanning electron microscopy, revealing diverse morphotypes in Staurosira and Staurosirella from the different lakes. Genetic analyses indicated a dominance of haplotypes that were assigned to fragilarioid taxa and less genetic diversity in other diatom taxa. The long rbcL_577 amplicon identified considerable diversification among haplotypes clustering within the Staurosira/Staurosirella genera, revealing 19 different haplotypes whose spatial distribution appears to be primarily related to the latitude of the lakes, which corresponds to a vegetation and climate gradient. Our rbcL markers are valuable tools Electronic supplementary material The online version of this article

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Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols

Cited by 245 publications

References 109 publications

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

Data rich, information poor? Phytobenthos assessment and the Water Framework Directive

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

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