Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations
Abstract
:1. Tracking Past Ecological Changes from Lakes and Catchments with Sedimentary DNA
1.1. Sedimentary DNA, a Powerful Proxy to Track Past Biodiversity Changes
1.2. sedaDNA to Study Past Vegetation Changes from Lake Catchment
1.3. sedaDNA to Detect Human and Animal Presence in the Lake Catchment
1.4. sedaDNA to Unravel Past Diversity and Composition of Lake Biota
1.5. Influence of Taphonomic Processes on the Burial and Persistence of sedaDNA
2. To What Degree does the sedaDNA Signal Represent Past Communities?
2.1. sedaDNA Data Compared to Historical, Archaeological and Monitoring Data
2.2. sedaDNA Data Compared to Other Sediment Proxies
2.3. Dead or Alive: What Makes Up the sedaDNA Pool?
3. State of the Art Lake sedaDNA Analyses
3.1. Criteria for the Selection of Lakes
3.2. Number of Sediment Cores to Collect for sedaDNA
3.3. Storage of Sediment Cores Prior to DNA Analysis
3.4. Number of Analytical Replicates to Perform for sedaDNA Research
3.5. Tracing Contamination of sedaDNA Samples
3.6. DNA Extraction Methods for sedaDNA Research
3.7. Sediment Amount to Use for DNA Extraction
3.8. Molecular Methods for Generating sedaDNA Data
3.9. DNA Markers and Reference Databases Used in Current sedaDNA Research
3.10. Bioinformatic Filtering and Analysis of sedaDNA Data
4. Recommendations
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A
Appendix A.1. Case Study A1—Effects of Sediment Type on PCR Amplification Success
By Kevin Nota 5 and Laura Parducci 5,31
Inhibition | DNA Concentration in ng/µL | |||||
---|---|---|---|---|---|---|
Sample | Age (Years BP) | (Before Cleaning) | Before Cleaning | After Cleaning | Difference | Recovery (%) |
Mon 163 | 31,191 | 0 | 0.21 | 0.16 | 0.05 | 0.75 |
Mon 157 | 28,151 | 0 | 3.94 | 3.06 | 0.88 | 0.78 |
Mon 144 | 21,676 | 1 | 0.25 | 0.2 | 0.06 | 0.78 |
Mon 136 | 17,467 | 5 | 0.38 | 0.37 | 0.01 | 0.98 |
Mon 127 | 14,476 | 5 | 0.42 | 0.42 | −0.01 | 1.02 |
Mon 121 | 14,181 | 5 | 0.38 | 0.38 | 0.01 | 0.98 |
Mon 115 | 13,933 | 20 | 0.37 | 0.38 | −0.01 | 1.04 |
Mon 100 | 12,779 | 2 | 0.66 | 0.6 | 0.06 | 0.91 |
Mon 064 | 10,271 | 10 | 0.89 | 0.88 | 0.01 | 0.99 |
Mon 063 | 10,008 | 2 | 0.83 | 0.81 | 0.02 | 0.98 |
Mon 050 | 7510 | 10 | 1.26 | 1.16 | 0.1 | 0.92 |
Mon 047 | 6964 | 5 | 1.07 | 0.97 | 0.1 | 0.91 |
Mon 040 | 5462 | 2 | 1.75 | 1.52 | 0.23 | 0.87 |
Mon 027 | 3425 | 10 | 1.28 | 1.17 | 0.11 | 0.91 |
Mon 025 | 3054 | 1 | 2.9 | 2.5 | 0.4 | 0.86 |
Mon 020 | 2061 | 1 | 2.38 | 2.07 | 0.31 | 0.87 |
Mean | 0.91 |
Material and Methods
Oligo Name | Sequence | GC% | Tm (°C) |
---|---|---|---|
In_CF_85 | ACGGAGTGCGGTCTTAATGG | 55 | 57.3 |
In_CR_85 | GGTACGGGTCTGTCGGATAG | 60 | 56.5 |
Inh_Template_Nota85 | ACGGAGTGCGGTCTTAATGGCGTTCAATTGCGTTAATTGACGGCTCGAGTGTCCCCTACATCTTGCTATCCGACAGACCCGTACC | 52.9 | 72.7 |
Plate | Sample Age Range | Number of Samples | Extraction Negatives | PCR Negatives | Index Cycles |
---|---|---|---|---|---|
Lane 1 | 14,149–31,191 yr BP | 4 × 2 × 40 | 4 × 2 × 4 | 4 | 10 |
Lane 2 | 11,520–14,132 yr BP | 4 × 2 × 40 | 4 × 2 × 4 | 4 | 16 |
Lane 3 | 1993–11,458 yr BP | 4 × 2 × 40 | 4 × 2 × 4 | 4 | 10 |
Appendix A.2. Case Study A2—Secondary Growth of Metabolically Versatile and Facultative Anaerobes during Sediment Storage and Handling of Sediment Cores
By Aurèle Vuillemin 7,8 and William D. Orsi 7,8
Appendix A.3. Case Study A3—Variability in Eukaryotic Inventories across Different DNA Extraction Protocols
By Isabelle Domaizon 29,30, Eric Capo 1, Charline Giguet Covex 2 and Irene Gregory-Eaves 18
Material and Methods
Lake | Age (yr BP) | Sediment Features |
---|---|---|
Lauzanier | −30 to −7 | 15 to 20% of organic matter (OM), 3 to 3.5% of carbonate, >75% of loss on ignition (LOI) residue |
Serre de l’Homme | −36 to −24 | 52 to 62% of OM, 2.3 to 2.5% of carbonates, >35.5% of LOI residue |
Bourget | −25 to −6 | 4 to 7% of organic matter (OM), 45 to 60 % of carbonates |
Léman | −30 to −8 | 4 to 9% of organic matter (OM), 35 to 58% of carbonates |
Appendix A.4. Case Study A4—Variability in Biological Groups across Different DNA Extraction Methods
By Kevin Nota 5 and Laura Parducci 5,31
Extraction | Mean (±sd) | Median | Min | Max |
---|---|---|---|---|
PS protocol | 557 ± 448 | 442 | 81 | 1531 |
exPS protocol | 34 ± 29 | 23 | 9 | 102 |
inPS protocol | 24 ± 25 | 15 | 0 | 94 |
aPS protocol | 24 ± 15 | 21 | 0 | 50 |
Material and Methods
Id | Location | Sediment Type | Age (yBP) | References |
---|---|---|---|---|
NER2 | North-east Russia | Peat-Permafrost | ~6000 | [125] |
NER11 | North-east Russia | Peat-Permafrost | ~8200 | [125] |
MON18 | Southern Italy | Lake | ~1993 | [284] |
MON78 | Southern Italy | Lake | ~11,562 | [284] |
NWF2 | North-west Finland | Peat | ~42,000 | [125] |
ATT2 | Southern Sweden | Lake | ~11,000 | [285] |
ATT25 | Southern Sweden | Lake | ~15,000 | [285] |
Primer Name | Target Taxa | Target Marker | Used Annealing Temperature | Length (bp) | References |
---|---|---|---|---|---|
Euka01For | Eukaryota | 18S rRNA | 59 °C | 48–777 | [288] |
Euka01Rev | |||||
Diat_rbcL_705F | Diatoms | rbcL | 49 °C | 76 | [105] |
Diat_rbcL_808R | |||||
Sper01For (g Taberlet) | Seed plants | trnL | 52 °C | 10–220 | [201] |
Sper01Rev (h Taberlet) | |||||
Atrh01For | Arthropoda | 16S mt DNA | 48 °C | 18–97 | |
Atrh01Rev | [167] | ||||
Vert01For | Vertebrata | 12S mt DNA | 49 °C | 56–132 | [289] |
Vert01Rev | |||||
A967F | Bacteria | 16S rRNA | 55 °C | 98 | [290] |
1046R |
Appendix A.5. Case Study A5—Effects of DNA Extraction Methods on the Diversity of the Plant DNA Signal
By Laura S. Epp 23, Liv Heinecke 19,20, Heike H. Zimmermann 19, Kathleen R. Stoof-Leichsenring 19 and Ulrike Herzschuh 19,21
Summary
Experimental Procedures
Sample | Lake | Geographical Area | Coordinates | Elevation (m asl) | Water Depth (m) | pH | Lake Area |
---|---|---|---|---|---|---|---|
11-CH06 | 11-CH06 | Siberia, Southern Taymyr Peninsula | 97.715861 N/70.667444 E | 103 | 4.8 | 6.42 | 0.05 km2 |
11-CH12 | 11-CH12 | 102.288566 N/ 72.398881 E | 60 | 14.3 | 7.5 | 0.03 km2 | |
11-CH17 | 11-CH17 | 102.235194 N/72.244486 E | 51 | 3.4 | 7.87 | 0.03 km2 | |
KK13_SS3 | Lake Karakul | Tajikistan, High Pamir Mountains | 39.01814 N/73.52910E | 3915 | 15.9 | 9.2 | 380 km2 |
KK13_SS7 | Lake Karakul | 39.02255 N/73.51955 E | 3915 | 20.4 | 9.2 | 380 km2 | |
KK13_SS8 | Lake Karakul | 73.51955 N/73.53254 E | 3915 | 13.8 | 9.2 | 380 km2 |
Extraction Kit | Kit Lysis Buffer | Phosphate Buffer (Extracellular) | Bulat Buffer + Proteinase K |
---|---|---|---|
FastDNA Spin Kit for Soil, 50 mL tubes (MP Biomedicals) | ~5 g | - | - |
FavorPrep Soil DNA Isolation Midi Kit (FavorGen) | ~5 g | - | - |
NucleoSpin Soil, Mini Kit (Macherey-Nagel) | ~0.25 g | ~5 g | - |
PowerMax Soil Kit (originally MoBio, now Qiagen) | ~5 g | ~5 g | ~5 g |
Results
Conclusions
Appendix A.6. Case Study A6—A Protocol for Ancient DNA Extraction from Calcite-Rich Minerogenic Lake Sediments
Peter D. Heintzman 6, Dilli P. Rijal 6, Antony G. Brown 6,11 and Inger G. Alsos 6
Sample | Depth (cm) | M/O | LOI (%) | XRF | Original Protocol | Optimised Protocol | Overlap | Fold Increase | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
550 | 950 | Ca/Ti | Si/Ti | Fe/Ti | Richness | Replic. | Richness | Replic. | Richness | Prop. | Richness | Replic. | |||
EG13_NEC | na | na | na | na | na | na | na | 0 | na | 0 | na | 0 | 0 | na | na |
EG13_NEC | na | na | na | na | na | na | na | 0 | na | 2 | 0.125 | 0 | 0 | na | na |
EG13_NEC | na | na | na | na | na | na | na | 1 | 0.125 | 0 | na | 0 | 0 | na | na |
EG13_NPC | na | na | na | na | na | na | na | 0 | na | 0 | na | 0 | 0 | na | na |
EG13_NPC | na | na | na | na | na | na | na | 0 | na | 0 | na | 0 | 0 | na | na |
EG13_L097 | 98.5 | O | 50.56 | 4.66 | 9.92 | 4.67 | 9.23 | 44 | 0.707 | 38 | 0.599 | 36 | 0.82 | 0.86 | 0.85 |
EG13_L141 | 142.5 | O | 79.16 | 2.64 | 7.53 | 0.58 | 5.89 | 32 | 0.539 | 35 | 0.496 | 26 | 0.81 | 1.09 | 0.92 |
EG13_L151 | 152.5 | M-O | 34.50 | 23.43 | 161.64 | 0.89 | 12.51 | 20 | 0.438 | 30 | 0.600 | 14 | 0.70 | 1.50 | 1.37 |
EG13_L153 | 154.5 | M-O | 31.83 | 25.08 | 197.30 | 1.10 | 13.94 | 11 | 0.227 | 26 | 0.543 | 9 | 0.82 | 2.36 | 2.39 |
EG13_L157 | 158.5 | M | 16.42 | 34.91 | 384.53 | 0.87 | 5.07 | 10 | 0.300 | 24 | 0.568 | 10 | 1.00 | 2.40 | 1.89 |
EG13_L161 | 162.5 | M | 12.36 | 33.73 | 238.23 | 1.01 | 2.01 | 9 | 0.611 | 27 | 0.551 | 8 | 0.89 | 3.00 | 0.90 |
Material and Methods
Appendix A.7. Case Study A7—Improvement of DNA Extraction Methods for the Detection of Catchment Mammal DNA Signal
By Charline Giguet-Covex 2, Francesco Gentile Ficetola 14,15 and Pierre Taberlet 6,15
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Organisms | Genic Regions | Length (bp) | References |
---|---|---|---|
plants | tnrL P6 loop | 49–188 | [201] |
mammals | 16S mtDNA | 60–84 | [31] |
fish | 12S gene | 163–185 | [221] |
zooplankton | 18S V7 | 100–110 | [222] |
zooplankton | COI gene | 313 | [223] |
microbial eukaryotes | 18S V1-V3 | 560 | [11] |
microbial eukaryotes | 18S V4 | 300–540 | [78] |
microbial eukaryotes | 18S V7 | 260 | [76] |
microbial eukaryotes | 18S V9 | 130 | [79] |
fungi | ITS2 region | 250–500 | [224] |
diatoms | rbcL gene | 67–76 | [105] |
diatoms | rbcL gene | 577 | [142] |
diatoms | 18S V4 | 400 | [225] |
archaea | 16S gene | 220 | [91] |
bacteria | 16S gene | 194 | [97] |
ammonium-oxidizing bacteria | amoA gene | 635 | [91] |
cyanobacteria | 16S gene | 400 | [74] |
methanotrophs | 16S gene | 111–200 | [97] |
dsDNA virus | mcp gene | 260 | [88] |
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Capo, E.; Giguet-Covex, C.; Rouillard, A.; Nota, K.; Heintzman, P.D.; Vuillemin, A.; Ariztegui, D.; Arnaud, F.; Belle, S.; Bertilsson, S.; et al. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary 2021, 4, 6. https://doi.org/10.3390/quat4010006
Capo E, Giguet-Covex C, Rouillard A, Nota K, Heintzman PD, Vuillemin A, Ariztegui D, Arnaud F, Belle S, Bertilsson S, et al. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. Quaternary. 2021; 4(1):6. https://doi.org/10.3390/quat4010006
Chicago/Turabian StyleCapo, Eric, Charline Giguet-Covex, Alexandra Rouillard, Kevin Nota, Peter D. Heintzman, Aurèle Vuillemin, Daniel Ariztegui, Fabien Arnaud, Simon Belle, Stefan Bertilsson, and et al. 2021. "Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations" Quaternary 4, no. 1: 6. https://doi.org/10.3390/quat4010006