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.
Plant diversity in the Arctic and at high altitudes strongly depends on and rebounds to climatic and environmental variability and is nowadays tremendously impacted by recent climate warming. Therefore, past changes in plant diversity in the high Arctic and high-altitude regions are used to infer climatic and environmental changes through time and allow future predictions. Sedimentary DNA (sedDNA) is an established proxy for the detection of local plant diversity in lake sediments, but still relationships between environmental conditions and preservation of the plant sedDNA proxy are far from being fully understood. Studying modern relationships between environmental conditions and plant sedDNA will improve our understanding under which conditions sedDNA is well-preserved helping to a.) evaluate suitable localities for sedDNA approaches, b.) provide analogues for preservation conditions and c.) conduct reconstruction of plant diversity and climate change. This study investigates modern plant diversity applying a plant-specific metabarcoding approach on sedimentary DNA of surface sediment samples from 262 lake localities covering a large geographical, climatic and ecological gradient. Latitude ranges between 25°N and 73°N and longitude between 81°E and 161°E, including lowland lakes and elevated lakes up to 5168 m a.s.l. Further, our sampling localities cover a climatic gradient ranging in mean annual temperature between -15°C and +18°C and in mean annual precipitation between 36 and 935 mm. The localities in Siberia span over a large vegetational gradient including tundra, open woodland and boreal forest. Lake localities in China include alpine meadow, shrub, forest and steppe and also cultivated areas. The assessment of plant diversity in the underlying dataset was conducted by a specific plant metabarcoding approach. We provide a large dataset of genetic plant diversity retrieved from surface sedimentary DNA from lakes in Siberia and China spanning over a large environmental gradient. Our dataset encompasses sedDNA sequence data of 259 surface lake sediments and three soil samples originating from Siberian and Chinese lakes. We used the established chloroplastidal P6 loop trnL marker for plant diversity assessment. The merged, filtered and assigned dataset includes 15,692,944 read counts resulting in 623 unique plant DNA sequence types which have a 100% match to either the EMBL or to the specific Arctic plant reference database. The underlying dataset includes a taxonomic list of identified plants and results from PCR replicates, as well as extraction blanks (BLANKs) and PCR negative controls (NTCs), which were run along with the investigated lake samples. This collection of plant metabarcoding data from modern lake sediments is still ongoing and additional data will be released in the future.
Arctic and alpine aquatic ecosystems are changing rapidly under recent global warming, threatening water resources by diminishing trophic status and changing biotic composition. Macrophytes play a key role in the ecology of freshwaters and we need to improve our understanding of long‐term macrophytes diversity and environmental change so far limited by the sporadic presence of macrofossils in sediments. In our study, we applied metabarcoding using the trnL P6 loop marker to retrieve macrophyte richness and composition from 179 surface‐sediment samples from arctic Siberian and alpine Chinese lakes and three representative lake cores. The surface‐sediment dataset suggests that macrophyte richness and composition are mostly affected by temperature and conductivity, with highest richness when mean July temperatures are higher than 12°C and conductivity ranges between 40 and 400 μS cm−1. Compositional turnover during the Late Pleistocene/Holocene is minor in Siberian cores and characterized by a less rich, but stable emergent macrophyte community. Richness decreases during the Last Glacial Maximum and rises during wetter and warmer climate in the Late‐glacial and Mid‐Holocene. In contrast, we detect a pronounced change from emergent to submerged taxa at 14 ka in the Tibetan alpine core, which can be explained by increasing temperature and conductivity due to glacial runoff and evaporation. Our study provides evidence for the suitability of the trnL marker to recover modern and past macrophyte diversity and its applicability for the response of macrophyte diversity to lake‐hydrochemical and climate variability predicting contrasting macrophyte changes in arctic and alpine lakes under intensified warming and human impact.
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