Sedimentary DNA Reveals Cyanobacterial Community Diversity over 200 Years in Two Perialpine Lakes

Abstract

We reconstructed cyanobacterial community structure and phylogeny using DNA that was isolated from layers of stratified sediments spanning 200 years of lake history in the perialpine lakes Greifensee and Lake Zurich (Switzerland). Community analysis based on amplification and sequencing of a 400-nucleotide (nt)-long 16S rRNA fragment specific to Cyanobacteria revealed operational taxonomic units (OTUs) capturing the whole phylum, including representatives of a newly characterized clade termed Melainabacteria, which shares common ancestry with Cyanobacteria and has not been previously described in lakes. The reconstruction of cyanobacterial richness and phylogenetic structure was validated using a data set consisting of 40 years of pelagic microscopic counts from each lake. We identified the OTUs assigned to common taxa known to be present in Greifensee and Lake Zurich and found a strong and significant relationship (adjusted R² = 0.89; P < 0.001) between pelagic species richness in water and OTU richness in the sediments. The water-sediment richness relationship varied between cyanobacterial orders, indicating that the richness of Chroococcales and Synechococcales may be underestimated by microscopy. PCR detection of the microcystin synthetase gene mcyA confirmed the presence of potentially toxic cyanobacterial taxa over recent years in Greifensee and throughout the last century in Lake Zurich. The approach presented in this study demonstrates that it is possible to reconstruct past pelagic cyanobacterial communities in lakes where the integrity of the sedimentary archive is well preserved and to explore changes in phylogenetic and functional diversity over decade-to-century timescales.

Importance: Cyanobacterial blooms can produce toxins that affect water quality, especially under eutrophic conditions, which are a consequence of human-induced climate warming and increased nutrient availability. Lakes worldwide have suffered from regular cyanobacterial blooms over the last century. The lack of long-term data limits our understanding of how these blooms form. We successfully reconstructed the past diversity of whole cyanobacterial communities over two hundred years by sequencing genes preserved in the sediments of two perialpine lakes in Switzerland. We identified changes in diversity over time and validated our results using existing data collected in the same two lakes over the past 40 years. This work shows the potential of our approach for addressing important ecological questions about the effects of a changing environment on lake ecology.

FIG 1

Map of Greifensee and Lake Zurich showing the sampling sites. The inset shows the location of the lakes within Switzerland. (Maps created with ESRI ArcMap version 10.3.1 using Swisstopo data.)

FIG 2

Photographs of oxidized varved sediments showing the depth profile of the upper 40 cm in a sediment core from lakes Greifensee (A) and Zurich (B). Arrows indicate the depths at which the sedDNA samples were collected and are identified by the corresponding year.

FIG 3

Phylogenetic tree of cyanobacterial OTUs based on Bayesian posterior probabilities. All 163 cyanobacterial 16S rRNA OTU reference sequences from the sediment samples of Greifensee and Lake Zurich were used to build the phylogeny. Chloroflexus aurantiacus was used as an outgroup, and 13 additional sequences obtained from GenBank and CyanoBase were added as references. Values at nodes indicate posterior probabilities calculated from 7,500,000 trees. The shapes indicate the samples from the two lakes, and the colors indicate the cyanobacterial order, with the nonphotosynthetic lineages (Melainabacteria and ML635J-21) grouped under the gray color. The 5 most abundant OTUs in Greifensee and the 3 most abundant OTUs in Lake Zurich (as presented in Fig. 4A and B) are identified with a star.

FIG 4

(Top) Proportions of cyanobacterial OTU richness within each order recovered from the sediments over the 6 years investigated between 1975 and 2010 in Greifensee (A) and Lake Zurich (B). (Bottom) Proportions of annual species richness (microscopic observations) within each order estimated from pelagic samples at the same time points from Greifensee (C) and Lake Zurich (D).

FIG 5

(Top) Proportions of reads of the 10 most abundant OTUs over the 6 years investigated between 1975 and 2010 in Greifensee (A) and Lake Zurich (B). (Bottom) Proportions of annual cell counts in the pelagic samples of the 10 most abundant species at the same time points in Greifensee (C) and Lake Zurich (D).

FIG 6

Linear model showing the relationship between annual cyanobacterial richness in the water and OTU richness in the sediments of Greifensee. The linear model, including pelagic species richness and lake identity as factors, was highly significant (P < 0.001; adjusted R² = 0.89; n = 12 between 1975 and 2010). The colored lines show the linear fit of the modeled lakes (Greifensee, y = 1.27x + 11.40, 1975 to 2006; Lake Zurich, y = 1.27x + 22.05, 1982 to 2006), and the gray dashed line is the 1:1 relationship.

FIG 7

Linear models showing the relationship of annual OTU richness estimated from the sediments and annual species richness estimated in water with samples grouped by order in Greifensee and Lake Zurich. The colors indicate the cyanobacterial order, and the gray dashed line represents the 1:1 line. The water-sediment richness relationship was significant in all orders (P < 0.02) except Nostocales (P = 0.09), and lake identity was a significant explanatory variable in the Chroococcales, Oscillatoriales, and Synechococcales models (P < 0.01).