Preservation of sedimentary plant DNA is related to lake water chemistry

Abstract

Little is currently known about preservation of plant DNA in lake sediments. Most prior information originates from laboratory experiments while systematic field‐based studies are still lacking. Here, we used the “g” and “h” universal primers for the P6 loop region of the chloroplast trnL (UAA) intron to amplify plant DNA from 219 lake surface sediments from China and Siberia. We introduce (i) the percentage of sequence counts with the best identity ≥95%, (ii) weighted average identity, (iii) weighted average DNA fragment length, and iv) rarefied richness of terrestrial seed plants of plant DNA metabarcoding as proxies for sedimentary DNA preservation and relate them to five environmental variables (lake water conductivity, lake water pH, mean July air temperature, and sampling depth, lake size) using boosted regression tree (BRT) analyses. Our results suggest that lake water chemical characteristics, that is, electrical conductivity and pH, are the most important variables for the preservation of plant DNA in lake sediments. Intermediate water conductivities (100–500 μS cm−1) and neutral to slightly alkaline water pH (7–9) may facilitate plant DNA preservation. Furthermore, deep lakes seem to support plant DNA preservation as indicated by relatively high rarefied richness. We also find high rarefied richness in small lakes compared with large lakes, but this result needs to be assessed by more studies in the future. None of our BRT models shows that mean July air temperature is a key variable to limit plant DNA preservation. To conclude, our results suggest that sedimentary DNA studies can preferentially select deep lakes characterized by intermediate water conductivities and neutral to slightly alkaline pH conditions.

Sedimentary DNA identifies modern and past macrophyte diversity and its environmental drivers in high‐latitude and high‐elevation lakes in Siberia and China

“…In our study, we detected 103 unique macrophyte ASVs from floating, submerged, and wetland taxa by using the trnL P6 loop as a metabarcode applied to surface and core sediments from Siberian and Chinese lakes. Despite the overall high number of recovered ASVs in our dataset, the macrophyte richness in the surfacesediment data varies strongly, which can be either caused by differences in DNA quality of the samples (Jia et al 2021) and related differences in metabarcoding success and/or by assembly rules that naturally affect macrophyte richness. The taxonomic resolution of the 103 ASVs is very good with a detection of 99% of ASVs to genus (67%) or species (32%) level, although the taxonomic resolution of the g-h amplified trnL P6 loop (Taberlet et al 2007) is lower compared to its encompassing longer trnL fragment (Zhu et al 2015).…”

“…Besides the dominance of a specific Stuckenia ASV, the globally distributed emergent macrophyte P. australis (common reed) is abundant in lakes with the highest conductivity (up to 57,000 μS cm À1 ) because it can withstand saline conditions (Köbbing et al 2013) and also because of the co-occurrence of beneficial rhizospheric microbial communities (Srivastava et al 2014). Differences in DNA preservation tested on a larger metabarcoding data of 219 surface samples (Stoof-Leichsenring et al 2020) that include aquatic and terrestrial plants indicate that conductivity and lake size significantly explain recovered total plant richness from surface sediment DNA (Jia et al 2021). Specifically, at high ion concentrations and partly warmer winter temperatures detected in a few Chinese lakes, poor sedDNA preservation might cause a decrease the recovery of the plant DNA signal in general (Jia et al 2021).…”

“…Differences in DNA preservation tested on a larger metabarcoding data of 219 surface samples (Stoof-Leichsenring et al 2020) that include aquatic and terrestrial plants indicate that conductivity and lake size significantly explain recovered total plant richness from surface sediment DNA (Jia et al 2021). Specifically, at high ion concentrations and partly warmer winter temperatures detected in a few Chinese lakes, poor sedDNA preservation might cause a decrease the recovery of the plant DNA signal in general (Jia et al 2021).…”

Sedimentary DNA of a human‐impacted lake in Western Canada (Cultus Lake) reveals changes in micro‐eukaryotic diversity over the past ~200 years

“…We recommend that more exploratory work of extracellular DNA be conducted to evaluate the potential of developing bioindicators from different environments (i.e., pelagic, littoral or terrestrial) across a wider range of lake conditions. For example, a recent study by Jia et al (2021) suggests that lake water conditions (i.e., pH and conductivity) can influence the preservation of extracellular DNA. More work is also needed to evaluate the congruence between extracellular and intracellular DNA fractions on sediment cores spanning longer time period to better understand the value of extracellular DNA when studying older sedDNA.…”

Compatibility of Diatom Valve Records With Sedimentary Ancient DNA Amplicon Data: A Case Study in a Brackish, Alkaline Tibetan Lake

“…Previous studies comparing the morphology and DNA-based methods for diatom identifications have worked with sediment cores from freshwater systems where the preservation of valves as well as DNA is expected to be favorable. A recent study about plant DNA preservation in the sediments suggested that lakes with pH 7-9 and conductivities with 100-500 μS/cm may have better preservation of sedimentary DNA compared to lakes with higher or lower values of latter measures (Jia et al, 2021). However, sedimentary DNA studies to identify diatom (Kang et al, 2021) and ostracod (Echeverría-Galindo et al, 2021) communities indicated the potential of DNA metabarcoding in the environmental settings of the lake Nam Co with conductivity >1,400 μS/cm and pH ~9.…”