Comparing Quantitative Methods for Analyzing Sediment DNA Records of Cyanobacteria in Experimental and Reference Lakes

Abstract

Sediment DNA (sedDNA) analyses are rapidly emerging as powerful tools for the reconstruction of environmental and evolutionary change. While there are an increasing number of studies using molecular genetic approaches to track changes over time, few studies have compared the coherence between quantitative polymerase chain reaction (PCR) methods and metabarcoding techniques. Primer specificity, bioinformatic analyses, and PCR inhibitors in sediments could affect the quantitative data obtained from these approaches. We compared the performance of droplet digital polymerase chain reaction (ddPCR) and high-throughput sequencing (HTS) for the quantification of target genes of cyanobacteria in lake sediments and tested whether the two techniques similarly reveal expected patterns through time. Absolute concentrations of cyanobacterial 16S rRNA genes were compared between ddPCR and HTS using dated sediment cores collected from two experimental (Lake 227, fertilized since 1969 and Lake 223, acidified from 1976 to 1983) and two reference lakes (Lakes 224 and 442) in the Experimental Lakes Area (ELA), Canada. Relative abundances of Microcystis 16S rRNA (MICR) genes were also compared between the two methods. Moderate to strong positive correlations were found between the molecular approaches among all four cores but results from ddPCR were more consistent with the known history of lake manipulations. A 100-fold increase in ddPCR estimates of cyanobacterial gene abundance beginning in ~1968 occurred in Lake 227, in keeping with experimental addition of nutrients and increase in planktonic cyanobacteria. In contrast, no significant rise in cyanobacterial abundance associated with lake fertilization was observed with HTS. Relative abundances of Microcystis between the two techniques showed moderate to strong levels of coherence in top intervals of the sediment cores. Both ddPCR and HTS approaches are suitable for sedDNA analysis, but studies aiming to quantify absolute abundances from complex environments should consider using ddPCR due to its high tolerance to PCR inhibitors.

Effects of temperature and oxygen on cyanobacterial DNA preservation in sediments: A comparison study of major taxa

“…The use of relative abundance data, however, does not correct for preservation biases between cyanobacterial taxa. In addition, there is still some uncertainty in using relative abundance data using sedaDNA (Mejbel et al, 2021). Interestingly, the high preservation capacity of Synechococcus has been noted in previous studies.…”

“…In addition, there is still some uncertainty in using relative abundance data using sedaDNA (Mejbel et al, 2021). Interestingly, the high preservation capacity of Synechococcus has been noted in previous studies.…”

Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long-term microscopy-based monitoring of the phytoplankton community

“…The reliability of sedDNA reconstructions depends on the extent of DNA degradation, which may occur at varying rates for different taxa in different environments (Capo et al ., 2021). Previous efforts have been made to explore DNA degradation patterns in dinoflagellates and bacillariophytes in an Antarctic lake core record (Boere et al ., 2011), and for cyanobacterial taxa within microcosms (Mejbel et al ., 2021). However, the extent of DNA degradation that different taxa may be subject to in temperate lake sediments requires further research, particularly for groups that were not well-represented by sedDNA, such as cryptophytes and haptophytes.…”

“…sedDNA offers many potential benefits compared to traditional palaeolimnological techniques. For example, a relatively high taxonomic resolution can be achieved, and high-throughput amplicon sequencing can process many hundreds or even thousands of samples relatively quickly (Bohmannet al ., 2022;Gong et al ., 2020;Mejbel et al ., 2021). A wider diversity of organisms can be studied using sedDNA, including those previously overlooked with microfossil analysis due to a lack of well-preserved and morphologically distinct remains (Domaizonet al ., 2017).…”

Molecular and Pigment Analyses Provide Comparative Results When Reconstructing Historic Cyanobacterial Abundances from Lake Sediment Cores

“…However, unlike diatoms, cyanobacteria have soft cell walls, which degrade quickly once the cell dies; therefore, the only proxies available to study them in sediment cores are the molecules they produce. Studies to date have targeted their pigments [10,[20][21][22][23][24][25], toxins (anatoxin, microcystin [24,26]), lipid biomarkers (e.g., 2-methylbacteriohopanetetrol as a possible biomarker for a freshwater strain of Synechococcus [27]), and now, their DNA [22,24,[27][28][29][30].…”