Dating sediment cores

are detected. Accurate dating of sediment sequences also permits calculation of Radiometric methods are now used routinely to date wetland sediment cores.
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Taking a Sediment Core

The PCR mixture was identical for the two species except for the concentrations of the reverse and forward primers: The PCR conditions for A. The PCR products were loaded onto 1. Several clones were obtained but only one clone of each species was retained for analysis.

The 14 C dating results of the sediment cores.

Quantification was performed using lambda DNA standards provided in the kit ranging from 2. For each target species, a standard curve was constructed with fold serial dilutions of the linearized plasmid containing the ITS1 rDNA sequence of the species. The experiments were conducted in well plates containing the standard curve dilutions in duplicate, the target samples and the negative controls composed of water instead of DNA that were both analyzed in triplicate.

A melting curve analysis was added at the end of each run to ensure specific A.

The real-time PCR mixture for S. The cycling conditions were: DNA amplifications of target species were considered positive if more than one out of the three replicates tested per sample was positive. Sanger sequencing of A. The semi-nested PCR assays were carried out only for A. This semi-nested PCR procedure yielded an amplicon of 93 bp and a sufficient A.

This method is usually used to calculate long-term trends or cycles from time series data, smoothing out short-term fluctuations in a dataset, and has been used in paleoecological studies e. Yu and Berglund The moving average of the A. These averaged values were used to produce the curves in Fig. The test was applied using the Kendall package in R software version 3. The Mann-Kendall trend test is a non-parametric test for monotonic trends, which is typically used to detect whether there is a significant increasing or decreasing trend in a time series Yue, Pilon and Cavadias In this test, the initial assumption is the null hypothesis H0 , which assumes that there is no trend in the data series over time.

The alternative hypothesis H 1 is that there is a significant trend increasing or decreasing over time. There was a general trend of an exponential decrease in Pb xs as expected due to the decay of the unsupported Pb. The Pb xs profile in the EE core showed the same trend: In both cores, the Pb xs decrease presented some irregularities.

This could be related to temporary changes in sedimentation intensity, which justified the use of the CSR constant rate of supply model for dating Fig. The sedimentary profile of Cs in the two cores presented the expected shape with two peaks nuclear weapon test fallout and Chernobyl in the deepest layers. In the DE core, Cs disappeared rapidly to negligible levels below the deepest peak. The EE core was too short to evaluate Cs disappearance; however, the expected peak of the second atmospheric fallout was observed.

In general, the sedimentary Cs peaks in the two cores mimicked the atmospheric fallout rather well, validating the Pb chronology Fig. For the EE core, S. Germinated diatom species belonged to Skeletonema spp. Other autotrophic Peridinium quinquecorne , Gymnodinium spp. Stars indicate the layers where the presence of the species was detected but quantitative data were below the LOQ of our real-time PCR assays.

The dashed lines indicate the limit layer of respective species germination. The black curves represent calculated moving average on the quantitative data. Total DNA concentrations extracted from the sediments ranged from 2. According to the S1, Supporting Information , with higher concentrations found in the first sediment layers of both cores. At 9 cm For real-time PCR tests, good linear relationships were found between the threshold cycle Ct and the initial number of copies 0.

To ensure specific amplifications, the melting temperature values Tm were systematically checked by analyzing the melting curves. In the case of S.

In these cases, the target species were considered present in the core layers, but it was not possible to quantify their ITS rDNA copy numbers. The presence of A.


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Nine and five sequences of 31—45 bp were obtained for DE and EE core layers, respectively. The sequences were aligned with other available sequences see File 1, Supporting Information; Fig. S3, Supporting Information and identified as A. Accurate DNA quantification of A. For both EE and DE, in the layers from which quantitative data were obtained, an increasing trend in the concentration of A.

This trend was visualized by the moving average calculation Fig. In particular, at EE, A. In layers from which non-quantitative data were obtained, the presence of A. These rDNA traces of A. At EE, a bimodal pattern of copy number abundance was evident. From the 9-cm layer to the top layer of the DE core, a decrease in copy number abundance was observed Fig.

In the layers for which non-quantitative data were obtained, the presence of S. At the Lanveoc station, A. At the Le Passage station, regular monitoring activities started when A. From to , no A. No bloom was observed in the area in but in , A.

Results of the CRS dating model when applied to four sediment cores | Download Table

A statistically significant increasing trend in A. The Daoulas time series was too short 3 years to analyze a multiannual trend, thus the Mann-Kendall test was not applied. When qualitatively compared over the overlapping period of analyses, the long-term data series of A. No monitoring of this taxon has ever been performed at the Daoulas station.

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Lower concentrations of Scrippsiella spp. At Lanveoc, Scrippsiella spp. At Le Passage, Scrippsiella spp. Lower abundances were registered during the following years see Fig. At both stations, no trend was detected by the Mann-Kendall coefficient for this taxon Lanveoc: Horizontal bars represent error on sediment dating. The paleoecological approach used in this study, based on paleogenetic analyses and ancient cyst revivification, provided historical data on two target dinoflagellate species over a time scale of about years.

The focus was mainly on the bloom-forming, toxic species A. Moreover, up to 31—year-old resting cysts were successfully revived from core sediments. Real-time PCR is a quantitative technique known to be highly sensitive, enabling species abundances to be estimated accurately in different environments even when the DNA target gene copy number is low.

Results of the CRS dating model when applied to four sediment cores from Florida lakes.

The advantage of real-time PCR is the fast processing of a large number of samples compared to cell or cyst counting microscopic procedures, which are time-consuming and often biased by taxonomic identification problems. Several studies have used real-time PCR to quantify the abundance of a large number of toxic phytoplankton species in seawater samples: Real-time PCR was the most appropriate method for our paleogenetic approach, which aimed to detect ancient genetic traces of the presence and abundance of the target species in the Bay of Brest.

Yet, when quantifying genetic material in old sediments, DNA degradation is a major issue to be taken into account. As the DNA fragments in our samples were relatively recent about years old and short about bp , the degradation and fragmentation issues should theoretically have been minimized. However, given the decreasing DNA concentrations revealed along both sampled cores, a potential degradation of the aDNA analyzed cannot be excluded. Furthermore, there is a high inter- and intra-species variability in the rDNA copy number of dinoflagellates. In fact, it is not certain that the 5.

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The longest cyst survival time observed in our study was 31—34 years for S. Assuming that the cyst mandatory dormancy period had passed in our samples, we consider that the unsuccessful germination in old sediment was more likely to be related to cyst viability. Over time, in old sediments, resting stages can undergo diagenetic processes and their survival depends on many physical and chemical conditions in the sediment including oxygen levels, temperature and pH Kremp and Anderson The reconstruction of preservation conditions in old sediments over time is very difficult and it is possible that some physical—chemical processes might have prevented cyst survival in these cores.

In addition, although different germination conditions different media and temperature conditions were tested and a final optimal combination temperature, nutrient concentration was found and systematically applied to all samples, it cannot be excluded that optimal germination conditions vary across sediments of different ages.