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

Abstract

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

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

“…That only two species were identified by the genetic approach, despite there being 37 different Staurosira-like sequences identified genetically and five Staurosira-like diatoms in the morphologically derived taxa list, originates primarily from the extremely limited number of references included in the EMBL database. The large diversity of Staurosiralike diatoms was already reported by Stoof- Leichsenring et al (2014Leichsenring et al ( , 2015 with respect to changes in haplotype appearances across tundra-northern taiga transects, and is corroborated by the results of our study. The taxonomy of Staurosira-like diatom taxa, as revealed by morphological analyses is still in revision (Williams and Round 1987;Paull et al 2008;Stoof-Leichsenring et al 2014).…”

“…The large diversity of Staurosiralike diatoms was already reported by Stoof- Leichsenring et al (2014Leichsenring et al ( , 2015 with respect to changes in haplotype appearances across tundra-northern taiga transects, and is corroborated by the results of our study. The taxonomy of Staurosira-like diatom taxa, as revealed by morphological analyses is still in revision (Williams and Round 1987;Paull et al 2008;Stoof-Leichsenring et al 2014). For example, one confusing reference description is S. elliptica (accession number HQ828193) and its likely synonym S. pinnata, used in morphological analyses.…”

“…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. In previous studies, this marker was used successfully on sediments from different habitats, such as fresh and saline African lakes (Stoof-Leichsenring et al 2012), freshwater lakes in Siberia (Stoof- Leichsenring et al 2014Leichsenring et al , 2015 and a high arctic lake in Greenland . Compared to ribosomal or mitochondrial markers, the specificity of the rbcL chloroplast marker to photosynthetic organisms strongly reduces the amplification of non-specific products, such as DNA from heterotrophic bacteria and fungi, which dominate sedimentary DNA samples.…”

“…Therefore, it was thought that a genetic approach, such as metabarcoding, might more easily reveal greater diatom diversity, including cryptic lineages. A particularly suitable diatom gene to study for environmental applications is the large subunit of the ribulose-1,5-bisphosphate-carboxylase/oxygenase (rbcL) gene (Stoof-Leichsenring et al 2014). This gene can be used not only to differentiate species, but because it is very variable within specific groups of diatoms, it provides information about putative intraspecific variation (Medlin et al 2012;Evans et al 2007).…”

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

“…A few genetic studies from the area find that the occurrence of intrageneric diatom lineages is linked to environmental conditions (i.e. vegetation in the catchment) rather than geographical constraints (Stoof‐Leichsenring et al, , ). Because species of a genus are generally composed of ecologically similar taxa, addressing diversity within genera will presumably result in stronger competition between taxa of the same genus than taxa of different genera.…”