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"Use of sedimentary DNA in reconstructing the past climates and
Ecological conditions"
Presented by:
Mr. Sangram Sahoo
Registration No.: 10BB24J64004
AcSIR-64-BS-AD-006
Advanced Course Phylogenetic Systematics/Cladistic Analysis and Palaeogenomics
● Sedimentary ancient DNA (sedaDNA) offers a novel retrospective approach to
reconstructing the history of marine ecosystems over geological timescales.
● The biological proxies used to reconstruct paleoceanographic and
paleoecological conditions were limited to organisms whose remains are
preserved in the fossil record.
● The development of ancient DNA analysis techniques substantially expands the
range of studied taxa, providing a holistic overview of past biodiversity.
● Future development of marine sedaDNA research is expected to dramatically
improve our understanding of how the marine biota responded to changing
environmental conditions.
Introduction
Bar chart showing the annual number
of published sedaDNA research articles
retrieved from Google Scholar and
cross-checked with the literature
database of the sedaDNA scientific
society.
Sources: Sec. Marine Ecosystem
Co-occurrence network map of
keywords found in abstracts
of sedaDNA research papers
● Marine sedaDNA research involves the analysis of genetic material preserved in marine
sediments from organisms that once lived in the water column or on the ocean floor.
● Several investigations in different sedimentary basins shed some light on the taphonomy of
sedaDNA in marine settings.
● The processes that regulate the accumulation and preservation of environmental DNA
(eDNA) in marine environments are more complex than in the freshwater-terrestrial system.
● This is because the marine environment with its surface and bottom water currents, sinking
water masses, lateral sediment transports, and sometimes very active benthic communities,
is more dynamic than freshwater systems.
Taphonomy and characteristics of
marine sedaDNA
Schematic illustration of eDNA taphonomic processes in the marine environment.
These processes involve eDNA distribution, degradation, and/or preferential
preservation during the transition from the pelagic to the benthic zones, and from the
water-sediment interface into subsurface sediment.
Sources: Sec. Marine Ecosystem
● The sediment core sampling strategy is the major difference between marine sedaDNA
and other studies involving ancient environmental DNA. In particular, sampling long
cores (> 10-meter-long) from depths of hundreds to thousands of meters below the sea
surface, while avoiding contamination is the main challenge of marine sedaDNA.
● Depending on the functional mechanisms that ensure penetration into the sediment, the
following coring methods are commonly used in marine sedaDNA research: gravity corer
(Coolen et al., 2013; Torti et al., 2018; De Schepper et al., 2019; More et al., 2021),
piston corer (Zimmermann et al., 2021; Armbrecht et al., 2022), multicorer (Coolen et
al., 2013; Lejzerowicz et al., 2013; De Schepper et al., 2019), and boxcorer (Coolen et
al., 2006).
Sediment coring
Bar chart showing the number of
published articles on
marine sedaDNA, indicating the age
of the sediment and the fragment
length of the analyzed amplicons,
variable: a range of fragment sizes is
obtained through metagenomics.
Treemap showing the number of published
articles targeting different taxonomic
groups of prokaryotes and eukaryotes in
marine sedaDNA.
Sources: Sec. Marine Ecosystem
Ecology
Sources: Sec. Marine Ecosystem
Ecology
• Due to the complexity of marine sediment composition and the wide range of target
organisms to be analyzed, choosing a universally optimal sedaDNA extraction method is
challenging (Armbrecht et al., 2020; Murchie et al., 2020; Kang et al., 2021). Extraction of
the highly degraded fragments of sedaDNA has to ensure efficient removal of inhibitors,
such as humic acids, while retaining a maximum amount of DNA in the solution.
sedaDNA extraction
• Most sedaDNA studies to date have utilized metabarcoding approaches for the
characterization of paleobiodiversity from sediment records.
• Metabarcoding consists of high-throughput sequencing of PCR-amplified marker genes,
thus the success of DNA metabarcoding depends on the selection of an appropriate DNA
marker.
• Ideally, such markers should have sufficiently conserved flanking primer-binding sites to
minimize taxonomic biases during PCR amplification (Liu et al., 2020), distinguish targeted
taxa, and possess a reference database for assigning taxonomy (Deagle et al., 2014).
Metabarcoding vs metagenomics
Potential and future applications of marine sedaDNA.
Sources: Sec. Marine Ecosystem
● Future developments in the marine sedaDNA research field will make it easier to
integrate paleogenetic signals preserved in the marine seafloor with other proxies.
● Based on the best understanding of each proxy, we can use the strengths of each
approach to their best advantage (i.e., complementary patterns of DNA metabarcoding
and morphology).
● The marine sedaDNA allows recovering a wide range of organisms that will provide
valuable material for searching for new paleo-bioindicators.
Future perspectives
• However, as an emerging approach, marine sedaDNA holds many challenges, and its ability
to recover reliable past biodiversity information needs to be carefully assessed.
• The quality assessment and quality control of sequences produced by sedaDNA
metabarcoding-metagenomics studies are particularly challenging given the potential
damage of DNA preserved in the sediments.
• It is critical to select a bioinformatic pipeline that addresses the challenges specific to the
recovery of sedaDNA signals.
Challenges
References
1. Nguyen, N. L., Devendra, D., Szymańska, N., Greco, M., Angeles, I. B., Weiner, A. K., ... & Pawłowska, J. (2023). Sedimentary ancient DNA: a
new paleogenomic tool for reconstructing the history of marine ecosystems. Frontiers in Marine Science, 10, 1185435.
2. Callahan B. J., Wong J., Heiner C., Oh S., Theriot C. M., Gulati A. S., et al. (2019). High-throughput amplicon sequencing of the full-length 16S
rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 47, e103–e103. doi: 10.1093/nar/gkz569
3. Allan E. A., Dibenedetto M. H., Lavery A. C., Govindarajan A. F., Zhang W. G. (2021). Modeling characterization of the vertical and temporal
variability of environmental DNA in the mesopelagic ocean. Sci. Rep. 11, 21273. doi: 10.1038/s41598-021-00288-5
4. Andruszkiewicz E. A., Sassoubre L. M., Boehm A. B. (2017). Persistence of marine fish environmental DNA and the influence of sunlight. PloS
One 12, e0185043. doi: 10.1371/journal.pone.0185043
5. Armbrecht L. H., Coolen M. J. L., Lejzerowicz F., George S. C., Negandhi K., Suzuki Y., et al. (2019). Ancient DNA from marine sediments:
precautions and considerations for seafloor coring, sample handling and data generation. Earth-Sci. Rev. 196, 102887. doi:
10.1016/j.earscirev.2019.102887
6. Armbrecht L., Eisenhofer R., Utge J., Sibert E. C., Rocha F., Ward R., et al. (2021a). Paleo-diatom composition from Santa Barbara Basin deep-
sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics. ISME Commun. 1, 66. doi: 10.1038/s43705-
021-00070-8
7. Armbrecht L., Hallegraeff G., Bolch C. J. S., Woodward C., Cooper A. (2021b). Hybridisation capture allows DNA damage analysis of ancient
marine eukaryotes. Sci. Rep. 11, 3220. doi: 10.1038/s41598-021-82578-6
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Use of sedimentary DNA in reconstructing the past climates and Ecological conditions

  • 1. "Use of sedimentary DNA in reconstructing the past climates and Ecological conditions" Presented by: Mr. Sangram Sahoo Registration No.: 10BB24J64004 AcSIR-64-BS-AD-006 Advanced Course Phylogenetic Systematics/Cladistic Analysis and Palaeogenomics
  • 2. ● Sedimentary ancient DNA (sedaDNA) offers a novel retrospective approach to reconstructing the history of marine ecosystems over geological timescales. ● The biological proxies used to reconstruct paleoceanographic and paleoecological conditions were limited to organisms whose remains are preserved in the fossil record. ● The development of ancient DNA analysis techniques substantially expands the range of studied taxa, providing a holistic overview of past biodiversity. ● Future development of marine sedaDNA research is expected to dramatically improve our understanding of how the marine biota responded to changing environmental conditions. Introduction
  • 3. Bar chart showing the annual number of published sedaDNA research articles retrieved from Google Scholar and cross-checked with the literature database of the sedaDNA scientific society. Sources: Sec. Marine Ecosystem Co-occurrence network map of keywords found in abstracts of sedaDNA research papers
  • 4. ● Marine sedaDNA research involves the analysis of genetic material preserved in marine sediments from organisms that once lived in the water column or on the ocean floor. ● Several investigations in different sedimentary basins shed some light on the taphonomy of sedaDNA in marine settings. ● The processes that regulate the accumulation and preservation of environmental DNA (eDNA) in marine environments are more complex than in the freshwater-terrestrial system. ● This is because the marine environment with its surface and bottom water currents, sinking water masses, lateral sediment transports, and sometimes very active benthic communities, is more dynamic than freshwater systems. Taphonomy and characteristics of marine sedaDNA
  • 5. Schematic illustration of eDNA taphonomic processes in the marine environment. These processes involve eDNA distribution, degradation, and/or preferential preservation during the transition from the pelagic to the benthic zones, and from the water-sediment interface into subsurface sediment. Sources: Sec. Marine Ecosystem
  • 6. ● The sediment core sampling strategy is the major difference between marine sedaDNA and other studies involving ancient environmental DNA. In particular, sampling long cores (> 10-meter-long) from depths of hundreds to thousands of meters below the sea surface, while avoiding contamination is the main challenge of marine sedaDNA. ● Depending on the functional mechanisms that ensure penetration into the sediment, the following coring methods are commonly used in marine sedaDNA research: gravity corer (Coolen et al., 2013; Torti et al., 2018; De Schepper et al., 2019; More et al., 2021), piston corer (Zimmermann et al., 2021; Armbrecht et al., 2022), multicorer (Coolen et al., 2013; Lejzerowicz et al., 2013; De Schepper et al., 2019), and boxcorer (Coolen et al., 2006). Sediment coring
  • 7. Bar chart showing the number of published articles on marine sedaDNA, indicating the age of the sediment and the fragment length of the analyzed amplicons, variable: a range of fragment sizes is obtained through metagenomics. Treemap showing the number of published articles targeting different taxonomic groups of prokaryotes and eukaryotes in marine sedaDNA. Sources: Sec. Marine Ecosystem Ecology Sources: Sec. Marine Ecosystem Ecology
  • 8. • Due to the complexity of marine sediment composition and the wide range of target organisms to be analyzed, choosing a universally optimal sedaDNA extraction method is challenging (Armbrecht et al., 2020; Murchie et al., 2020; Kang et al., 2021). Extraction of the highly degraded fragments of sedaDNA has to ensure efficient removal of inhibitors, such as humic acids, while retaining a maximum amount of DNA in the solution. sedaDNA extraction
  • 9. • Most sedaDNA studies to date have utilized metabarcoding approaches for the characterization of paleobiodiversity from sediment records. • Metabarcoding consists of high-throughput sequencing of PCR-amplified marker genes, thus the success of DNA metabarcoding depends on the selection of an appropriate DNA marker. • Ideally, such markers should have sufficiently conserved flanking primer-binding sites to minimize taxonomic biases during PCR amplification (Liu et al., 2020), distinguish targeted taxa, and possess a reference database for assigning taxonomy (Deagle et al., 2014). Metabarcoding vs metagenomics
  • 10. Potential and future applications of marine sedaDNA. Sources: Sec. Marine Ecosystem
  • 11. ● Future developments in the marine sedaDNA research field will make it easier to integrate paleogenetic signals preserved in the marine seafloor with other proxies. ● Based on the best understanding of each proxy, we can use the strengths of each approach to their best advantage (i.e., complementary patterns of DNA metabarcoding and morphology). ● The marine sedaDNA allows recovering a wide range of organisms that will provide valuable material for searching for new paleo-bioindicators. Future perspectives
  • 12. • However, as an emerging approach, marine sedaDNA holds many challenges, and its ability to recover reliable past biodiversity information needs to be carefully assessed. • The quality assessment and quality control of sequences produced by sedaDNA metabarcoding-metagenomics studies are particularly challenging given the potential damage of DNA preserved in the sediments. • It is critical to select a bioinformatic pipeline that addresses the challenges specific to the recovery of sedaDNA signals. Challenges
  • 13. References 1. Nguyen, N. L., Devendra, D., Szymańska, N., Greco, M., Angeles, I. B., Weiner, A. K., ... & Pawłowska, J. (2023). Sedimentary ancient DNA: a new paleogenomic tool for reconstructing the history of marine ecosystems. Frontiers in Marine Science, 10, 1185435. 2. Callahan B. J., Wong J., Heiner C., Oh S., Theriot C. M., Gulati A. S., et al. (2019). High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 47, e103–e103. doi: 10.1093/nar/gkz569 3. Allan E. A., Dibenedetto M. H., Lavery A. C., Govindarajan A. F., Zhang W. G. (2021). Modeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean. Sci. Rep. 11, 21273. doi: 10.1038/s41598-021-00288-5 4. Andruszkiewicz E. A., Sassoubre L. M., Boehm A. B. (2017). Persistence of marine fish environmental DNA and the influence of sunlight. PloS One 12, e0185043. doi: 10.1371/journal.pone.0185043 5. Armbrecht L. H., Coolen M. J. L., Lejzerowicz F., George S. C., Negandhi K., Suzuki Y., et al. (2019). Ancient DNA from marine sediments: precautions and considerations for seafloor coring, sample handling and data generation. Earth-Sci. Rev. 196, 102887. doi: 10.1016/j.earscirev.2019.102887 6. Armbrecht L., Eisenhofer R., Utge J., Sibert E. C., Rocha F., Ward R., et al. (2021a). Paleo-diatom composition from Santa Barbara Basin deep- sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics. ISME Commun. 1, 66. doi: 10.1038/s43705- 021-00070-8 7. Armbrecht L., Hallegraeff G., Bolch C. J. S., Woodward C., Cooper A. (2021b). Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes. Sci. Rep. 11, 3220. doi: 10.1038/s41598-021-82578-6