Figure 5 - uploaded by Eric Capo
Content may be subject to copyright.
(A) Case study A3. Proportion of reads within microbial eukaryotic and metazoan assemblages for DNA extracted with the NucleoSpin protocol (intracellular and extracellular DNA) and Taberlet 2012 protocol (extracellular DNA) from sediments collected in four lakes (Bourget (LDB), Geneva (LEM), Lauzanier (LAZ), Serre de l´Homme (SDH)). For each extraction protocol, two DNA extracts were obtained. (B) Case study A4. qPCR Amplification success (quantification cycle (Cq) value) of DNA extracts obtained with different extraction methods: the standard PowerSoil kit protocol (PS protocol), a Powersoil protocol coupled with Phosphate Buffer to extract the extracellular (exPS protocol) and intracellular DNA (inPS protocol) fractions. Lower Cq values imply a higher qPCR amplification success (i.e., a lower number of PCR cycles necessary to detect a signal above the fluorescence background). (C) Case study A5. Number of plant molecular taxa identified in six surface sediments after DNA extraction with four different protocols: FastDNA ® Spin Kit for soil (FD), Favor Prep Soil DNA Isolation Midi Kit (FP), Nucleospin Soil Kit (NS) and PowerMax Soil DNA Isolation Kit (PM). The samples were obtained from three small lakes from the Southern Taymyr Peninsula, Siberia, and from three locations within Lake Karakul, Pamir Mountains, Tajikistan. The molecular taxa were split into three categories: terrestrial plants,
Source publication
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building...
Contexts in source publication
Context 1
... this box we describe the main findings of five case studies and for each of them additional information is presented in Appendix A. The case study A3 compares eukaryotic inventories obtained using a protocol extracting both exDNA and inDNA (NucleoSpin protocol) and a protocol favoring exDNA extraction (Taberlet 2012 protocol). We showed that the composition of eukaryotes varies depending on the extraction protocol used, even when considering the high variability in the signal recovered from each lake ( Figure 5A). This is also the case in terms of richness ( Figure A3 in Appendix A). ...
Context 2
... striking finding is that the extraction of total DNA with the NucleoSpin protocol appeared to be more efficient for detecting rotifer DNA than the Tarberlet2012 protocol for extracting exDNA, most likely because of the improved extraction of DNA from rotifer eggs with the lysis buffer from the NucleoSpin protocol. The case study A4 revealed that the qPCR amplification of several aquatic and terrestrial taxa targeted (bacteria, diatoms, eukaryotes, plants, arthropods and vertebrates) led to similar amplification levels (low quantification cycle (Cq) values correspond to higher amplification success)-when comparing inDNA and exDNA fractions obtained from a modified Powersoil protocol, with the exception of arthropods that were found to be amplified preferentially from intracellular DNA ( Figure 5B). In addition, the use of the unmodified Powersoil protocol for extracting total DNA was more efficient for detecting and amplifying sedaDNA from several biological groups (average Cq values lower). ...
Context 3
... (Taberlet2012) were investigated both for use with the NucleoSpin kit and the PowerMax Soil kit. For samples from lakes surrounded by a high taxonomic diversity of terrestrial plants, distinct differences in the number of plant molecular taxa retrieved were observed between extraction protocols, with the unmodified PowerMax kit revealing the highest number of Molecular Operational Taxonomic Units (MOTUs) ( Figure 5C). In our case study A6, we show that a modified DNA extraction protocol designed to release the mineral-bound sedaDNA from calcitic minerals using EDTA-based chelation provide higher richness estimates of plant assemblages in calcite-rich sediments but was comparable for organic-rich sediments, though with a lower level of reproducibility ( Figure 5D). ...
Context 4
... samples from lakes surrounded by a high taxonomic diversity of terrestrial plants, distinct differences in the number of plant molecular taxa retrieved were observed between extraction protocols, with the unmodified PowerMax kit revealing the highest number of Molecular Operational Taxonomic Units (MOTUs) ( Figure 5C). In our case study A6, we show that a modified DNA extraction protocol designed to release the mineral-bound sedaDNA from calcitic minerals using EDTA-based chelation provide higher richness estimates of plant assemblages in calcite-rich sediments but was comparable for organic-rich sediments, though with a lower level of reproducibility ( Figure 5D). Finally, while investigating the number of positive PCR replicates required for the analyses of domesticated mammal DNA (ovine and bovine) in the case study A7, we reported higher amplification success when using Amicon filters coupled with the Taberlet2012 protocol relative to using the standard approach (Taberlet2012 protocol) ( Figure 5E). ...
Context 5
... our case study A6, we show that a modified DNA extraction protocol designed to release the mineral-bound sedaDNA from calcitic minerals using EDTA-based chelation provide higher richness estimates of plant assemblages in calcite-rich sediments but was comparable for organic-rich sediments, though with a lower level of reproducibility ( Figure 5D). Finally, while investigating the number of positive PCR replicates required for the analyses of domesticated mammal DNA (ovine and bovine) in the case study A7, we reported higher amplification success when using Amicon filters coupled with the Taberlet2012 protocol relative to using the standard approach (Taberlet2012 protocol) ( Figure 5E). The samples were obtained from three small lakes from the Southern Taymyr Peninsula, Siberia, and from three locations within Lake Karakul, Pamir Mountains, Tajikistan. ...
Context 6
... sites-The study sites are listed in Table A6. DNA extraction-Three extractions protocols were conducted on seven sediment samples in duplicate; see Figure A5 for the extraction schemes. All extractions were performed from ca 0.25 g of sediments. ...
Context 7
... minerogenic sediment samples (M, M-O), with an elevated LOI950 (>20%) and Ca/Ti (>100), exhibited a 1.5-3.0-fold increase in richness, with PCR replicability increasing by an average of 64%, when the optimized protocol was applied (Table A10, Figure 5D in the main text). The majority of taxa detected in the minerogenic sediment samples using the original protocol are also recovered with the optimized protocol (mean of 85%, Table A10). ...
Context 8
... addition to these general patterns, the two protocols give contrasting results for the inferred first occurrence of key woody taxa, with crowberry (Empetrum nigrum), blueberry (Vaccinium myrtillus), lingonberry (V. vitis-idaea), pine (Pinus sylvestris), and alder (Alnus) first appearing within an 8-cm interval between 154.5 and 142.5 cm, based on data from the original protocol ( Figure 5D in main text). However, the optimized protocol indicates that crowberry was already present in the catchment during the early postglacial (162.5 cm), with blueberry and lingonberry appearing from at least 158.5 cm. ...
Context 9
... the both approaches, we obtained Bos and Ovis sequences only from the Roman and from the recent sediment samples. Overall, for both species the amplification rate was higher using the AmTaberlet2012 method than the standard Taberlet2012 method ( Figure 5E in the main text). With the AmTaberlet2012 method, the detection probability of both cattle and sheep was 0.562 (95% confidence intervals: 0.32-0.78). ...
Citations
... As a consequence of their biotope, aquatic macrophytes are readily incorporated into sediment, and are therefore especially well represented in sedimentary ancient DNA (sedaDNA) records Capo et al., 2021). Thus, combining a molecular palaeorecord of macrophytes with their known functional traits could allow for the reconstruction of past environmental conditions Dalla Vecchia et al., 2020;Dar et al., 2014). ...
... This can assist in unlocking the bottleneck to access the large potential of metagenomics for palaeoecology of aquatic macrophytes and other taxa Kjaer et al. 2022). We can expect to see a continued increase in eDNA publications in the near future (Capo et al., 2021), as methods are refined and reference libraries are supplemented. Metabarcoding is the least expensive of all three methods and requires smaller reference libraries. ...
Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico-chemical conditions. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.
... Sediments integrate material from throughout lake ecosystems and should preserve source DNA via physical sorption to particles and the absence of light and oxygen within the sedimentary matrix, including material from all cyanobacteria genera (Capo et al., 2021). ...
... However, these factors often are relatively constant through time such that the production and deposition of labile biomarkers often are highly correlated in retrospective comparisons of centennial duration (Leavitt & Findlay, 1994). In addition, techniques for collecting, extracting and amplifying sedDNA are being refined continually (Capo et al., 2021;Domaizon et al., 2013Domaizon et al., , 2017Pal et al., 2015;Tse et al., 2018), such that it is now possible to both reconstruct changes in taxonomic composition (e.g., high-throughput sequencing [HTS]) and quantify the occurrence of genes with known functions (e.g., quantitative polymerase chain reaction [qPCR] or droplet digital PCR [ddPCR]) (Mejbel et al., 2021;Pilon et al., 2019) to estimate both the abundance and function of primary producer populations. When studying cyanoHABs, this dual approach can be used to reconstruct changes in cyanobacterial communities and determine the prevalence of genes responsible for the production of cyanotoxins. ...
... sedDNA is becoming more widely used in palaeolimnology, but there are currently some uncertainties surrounding the deposition and taphonomy of DNA in lakes (Capo et al ., 2021;2022). The extent and rate of DNA degradation may vary among taxa and depend upon the state in which DNA is deposited. ...
... Cryptophytes could therefore be expected to be detected using sedDNA, but similar to the present study, Capo et al . (2015) also reported that cryptophytes were poorly represented by sedDNA and suggested that the absence of a cell wall made their DNA vulnerable to degradation, and their high nutritional content made them vulnerable to grazing by zooplankton so that cells did not reach the sediment surface (Capo et al ., 2015;Capo et al ., 2021). Haptophytes were also poorly represented by sedDNA, and an underrepresentation of haptophytes in Lake Bourget, France, as measured by sedDNA has previously been reported (Capoet al ., 2015). ...
... Haptophytes were not consistently counted throughout the monitoring scheme, so determining whether this group was underrepresented because they experienced greater rates of DNA degradation, or because they had a low abundance in Esthwaite Water is challenging. 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). ...
Palaeolimnological records provide valuable information about how phytoplankton respond to long-term drivers of environmental change. Traditional palaeolimnological tools such as microfossils and pigments are restricted to taxa that leave sub-fossil remains, and a method that can be applied to the wider community is required. Sedimentary DNA (sedDNA), extracted from lake sediment cores, shows promise in palaeolimnology, but validation against data from long-term monitoring of lake water is necessary to enable its development as a reliable record of past phytoplankton communities. To address this need, 18S rRNA gene amplicon sequencing was carried out on lake sediments from a core collected from Esthwaite Water (English Lake District) spanning ~105 years. This sedDNA record was compared with concurrent long-term microscopy-based monitoring of phytoplankton in the surface water. Broadly comparable trends were observed between the datasets, with respect to the diversity and relative abundance and occurrence of chlorophytes, dinoflagellates, ochrophytes and bacillariophytes. Up to 20% of genera identified in the microscopy record were also detected using sedDNA, and sedDNA revealed a previously undetected community of phytoplankton. However, a substantial proportion of genera identified by microscopy were not detected using sedDNA, highlighting the current limitations of the technique that require further development such as reference database coverage. These results suggest that sedDNA can be used as an effective record of past phytoplankton communities, at least over timescales of less than 100 years, but the taphonomic processes which may affect its reliability, such as the extent and rate of deposition and DNA degradation, require further research.
... We also found that 29.4 % (11,851/41,018) of the overall OTU richness corresponded to unclassified eukaryotic sequences which might be due to the relatively short length of the amplified region used here. Since our study corresponded to the transfer of materials from land to the sea, we chose the V7 region of the 18S rRNA gene, which has proven its interest in addressing past terrestrial and aquatic biodiversity (Capo et al., 2016;Capo et al., 2021;Gauthier et al., 2022). Recently, Siano and colleagues showed that even if V7 and V4 regions give similar diversity for eukaryotic paleocommunities, the V4 barcode allowed the identification of more groups (Siano et al., 2021). ...
Land use change and anthropogenic forcing can drastically alter the rates and patterns of sediment transport and modify biodiversity and ecosystem functions in coastal transition zones, such as the coastal ecosystems. Molecular studies of sediment extracted DNAs provide information on currently living organisms within the upper layers or buried from various periods of time, but might also provide knowledge on species dynamics, replacement and turnover. In this study, we evaluated the eukaryotic communities of a marine core that present a shift in soil erosion that was linked to glyphosate usage and correlated to chlordecone resurgence since 2000. We show differences in community composition between samples from the second half of the last century and those from the last two decades. Temporal analyses of the relative abundance, alpha diversity, and beta diversity for the two periods demonstrated different temporal dynamics depending on the considered taxonomic group. In particular, Ascomycetes showed a decrease in abundance over the most recent period associated with changes in community membership but not community structure. Two photosynthetic groups, Bacillariophyceae and Prasinophytes clade VII, showed a different pattern with an increase in abundance since the beginning of the 21st century with a decrease in diversity and evenness to form more heterogeneous communities dominated by a few abundant OTUs. Altogether, our data reveal that agricultural usages such as pesticide use can have long-term and species-dependent implications for microeukaryotic coastal communities on a tropical island.
... However, false positives/negatives are still an issue. Nevertheless, biomonitoring the change through sediments is a promise for paleoecology (Capo et al., 2021). A recent review of methods, protocols, and recommendations for standardization was made by Pawlowski et al. (2022). ...
The COI gene, colloquially named the DNA barcode, is a universal marker for species identification in the animal kingdom. Nevertheless, due to the taxonomic impediment, there are various proposals for molecular operational taxonomic units (MOTUs) because high-throughput sequencers can generate millions of sequences in one run. In the case of freshwater systems, it is possible to analyze whole communities through their DNA using only water or sediment as a sample. Using DNA barcodes with these technologies is known as metabarcoding. More than 90% of studies based on eDNA work with MOTUs without previous knowledge of the biodiversity in the habitat. Despite this problem, it has been proposed as the future for biomonitoring. All these studies are biased toward the Global North and focused on freshwater macrofaunae. Few studies include other regions of the world or other communities, such as zooplankton and phytoplankton. The future of biomonitoring should be based on a standardized gene, for example, COI, the most studied gene in animals, or another secondary consensual gene. Here, we analyzed some proposals with 28S or 12S. The studies on eDNA can focus on analyses of the whole community or a particular species. The latter can be an endangered or exotic species. Any eDNA study focused on a community study should have a well-documented DNA baseline linked to vouchered specimens. Otherwise, it will be tough to discriminate between false positives and negatives. Biomonitoring routines based on eDNA can detect a change in a community due to any perturbation of the aquatic ecosystem. Also, it can track changes along the history of an epicontinental environment through the analyses of sediments. However, their implementation will be complex in most megadiverse Neotropical countries due to the lack of these baselines. It has been demonstrated that a rapid functional construction of a DNA baseline is possible, although the curation of the species can take more time. However, there is a lack of governmental interest in this kind of research and subsequent biomonitoring.
... In contrast to the fairly long history of ancient DNA research, which began in the 1980s (e.g. Higuchi et al. 1984;Mullis et al. 1986;Pääbo 1989), sedaDNA research is a relatively young field that is rapidly gaining importance in palaeoenvironmental studies as its provenance and taphonomy become better understood (Giguet-Covex et al. 2019;Edwards 2020;Capo et al. 2021). The analysis of sedaDNA can follow three approaches: (i) DNA metabarcoding (Taberlet et al. 2012), (ii) shotgun metagenomic analyses (Pedersen et al. 2016) and (iii) target enrichment capture (Capo et al. 2021). ...
... Higuchi et al. 1984;Mullis et al. 1986;Pääbo 1989), sedaDNA research is a relatively young field that is rapidly gaining importance in palaeoenvironmental studies as its provenance and taphonomy become better understood (Giguet-Covex et al. 2019;Edwards 2020;Capo et al. 2021). The analysis of sedaDNA can follow three approaches: (i) DNA metabarcoding (Taberlet et al. 2012), (ii) shotgun metagenomic analyses (Pedersen et al. 2016) and (iii) target enrichment capture (Capo et al. 2021). DNA metabarcoding techniques use polymerase chain reaction (PCR) amplification of a short (often <100 bp) fragment of the genome found across the range of a target taxonomic group. ...
Lake and peat sediments are frequently used to reconstruct palaeoclimate records from all continents using a variety of proxy techniques. This chapter explores the advances that have occurred in the last 20 or more years for using lake and peat sediments to reconstruct past climate change. It demonstrates the impact these advances have had for palaeoclimate research, and implications for archaeology. Fossilized insect remains are often abundant in a wide range of sediments, including lake, river, and peat deposits. Fire is a natural disturbance in many ecosystems, and lake sediments often contain charcoal that can be used to infer fire dynamics. Ombrotrophic bogs have accumulated deep peat deposits throughout the last 10 000 years in temperate latitudes and elsewhere around the world. The chapter focuses on the research that underpins estimates of past palaeoclimate variability as inferred from peatlands.
... Using conventional genome and NGS sequencing, more than 200 articles have been published that deal with understanding ancient human remains, plants, microbes, fungi, bacteria, viruses and larger mammals, and the response of these individual biotic elements to environmental changes 40 . About 20 articles every year utilize lake sediment DNA to provide a time series of complete terrestrial and aquatic holobiome to Late Pleistocene-Holocene climate and environmental change 45 . ...
... Therefore, the potential to reconstruct past cyanobacteria variability based on classical fossil-based proxies is limited. Within the last decade, a variety of DNA-based paleolimnological methods have emerged as novel and complementary proxies for use in reconstructing past cyanobacteria variability at improved accuracy 9 , including physiologically dormant, active, and inactive organisms buried in sediments 20 . Major advantages of DNA-based approaches include their high phylogenetic resolution and their reliable coverage of the entire cyanobacteria phylum preserved in sediment archives 18,21,22 . ...
... Our multi-proxy study based on cyanobacteria DNA and biomarker analyses provides evidence of the long-term preservation of lake cyanobacteria DNA in lake sediments dating back to ca. 11,400 years. A foremost challenge to sedaDNA data interpretation is the current limited knowledge of taphonomic processes affecting DNA during the transport into sediments, and preservation of DNA in sediments under prevailing environmental conditions 20 . We have previously shown that the mainly anoxic cold water-sediment interface in Lake Tiefer See promotes DNA preservation after incorporation 22,30 . ...
Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia. Analysis of sedimentary DNA through time in a German lake shows a spike in cyanobacteria abundance coinciding with human activity in the Bronze Age.
... According to the evolution and trend analysis of keywords, the Keywords represented by "diversity," "holocene," and "climate change" have become hot topics in recent years. However, most studies on biodiversity using sedDNA have paid attention to lake systems (Capo et al. 2021), and those on marine systems are scarce (Armbrecht et al. 2019). Compared with freshwater systems, marine systems exhibit higher salinity and ion concentrations, higher pH, and more stable temperatures, as well as a combination of these factors, which favors the well-preservation of sedDNA in the ocean (Collins et al. 2018). ...
Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a “Research Weaving” method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.
... Specifically, the application of eDNA metabarcoding improves the capability to simultaneously capture various biological components encompassing multiple trophic levels (Djurhuus et al., 2020). Indeed, the analysis of ancient eDNA preserved in sediment (sedaDNA) enables the reconstruction of the present-day to past biological communities and paleo-environmental conditions (Pedersen et al., 2015;Brown and Blois, 2016;Capo et al., 2021). In lakes sediments, prokaryote communities (cyanobacteria) were targeted to evaluate temperature rise and eutrophication effects (Monchamp et al., 2017), while changes in the composition of micro-eukaryotic communities allowed to follow anthropogenic impacts in Alpine lakes (Keck et al., 2020). ...
The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.
