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

Abstract

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.

Lake-depth related pattern of genetic and morphological diatom diversity in boreal Lake Bolshoe Toko, Eastern Siberia

“…diatom diversity from sedimentary samples (25,26) by using PCR with barcoded primers. Preparation of PCR samples for DNA sequencing are described in (24). Based on the metafast protocol, the pool of PCR samples was sequenced with parallel high-throughput paired-end (2x125 bp) amplicon sequencing on the Illumina HiSeq 2000 platform (Illumina Inc.) using an external sequencing service (Fasteris SA, Switzerland).…”

“…Taxonomic assignment with the function ecotag was performed using a database created with ena release128. Details of the bioinformatical analyses of the data are given in [24]. After using the OBITools pipeline, the final results were entered into a spreadsheet and further filtered manually.…”

“…Especially regarding within-species/genus variations, whereas several genetic approaches addressing diatom diversity on lower taxonomic levels have uncovered cryptic and hidden diversity in similar morphotypes [17][18][19]. With the advent of the metabarcoding approach combined with advancing high-throughput next-generation sequencing techniques, diatom compositions have been retrieved with various genetic markers and from different environments [20][21][22][23][24]. Especially differences in intra/inter-specific variations have been detected in sedimentary DNA (sedDNA) from surface-and core-sediment samples by applying a short, but specific, chloroplast rbcL metabarcode [25,26].…”

“…This ability for in-depth taxonomic identification in some diatom groups offers a great advantage for the analysis of minor differences between lakes, but also within-lake variability of ecologically indicative minute diatoms. In general, genetic and morphological investigations of diatoms from water or sediment samples show a good overlap between the overall taxa composition, although genetic studies show stronger differences in the relative abundance of sequence reads per sample and indicate higher diversity as well as assigning taxa to a higher taxonomic level depending on the completeness of the reference database [22,24,27]. Besides retrieving taxonomic community compositions by metabarcoding, phylogenetically informative genetic markers also provide an estimation of the phylogenetic diversity [28], which is limited in short barcodes but can be sufficient to display phylogenetic patterns within genera [29].…”

Phylogenetic diversity and environment form assembly rules for Arctic diatom genera—A study on recent and ancient sedimentary DNA

“…The large subunit of the Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (rbcL) has been used frequently for phylogenetic analyses (Guo, Sui, Zhang, Ren, & Liu, ; Theriot, ), but is most powerful in determining lower taxonomic levels and thus has been used to identify intragenus and intraspecies genetic diversity and diversification (Abarca, Jahn, Zimmermann, & Enke, ; Evans, Wortley, & Mann, ; Hamsher, Evans, Mann, Poulickova, & Saunders, ; Kermarrec, Bouchez, Rimet, & Humbert, ). Moreover, short rbcL metabarcodes have been successfully applied for diatom diversity assessment (Dulias, Stoof‐Leichsenring, Pestryakova, & Herzschuh, ; Rimet, Vasselon, A.‐Keszte, & Bouchez, ). Combining taxonomic with phylogenetic diversity retrieved from sedimentary DNA archives is a fairly new approach.…”