Geochemical identification of potential DNA-hotspots and DNA-infrared fingerprints in lake sediments

Kanbar, Hussein; Olajos, Fredrik; Englund, Göran; Holmboe, Michael

doi:10.1016/j.apgeochem.2020.104728

Cited by 27 publications

(29 citation statements)

References 46 publications

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“…InDNA is likely to be more protected inside protective resting stages such as cysts or spores, cell membranes, or lignins, but can also be attacked by nucleases present in the cells. In contrast, exDNA released into the environment after cell lysis can be quickly adsorbed on clay minerals, which significantly promotes preservation by decreasing chemical and physical degradation processes [101] and making its molecules less accessible as a food source for indigenous sediment bacteria [190]. One of the protocols that allows desorption of exDNA fragments bound to minerogenic particles is described in Taberlet et al [191] named hereafter the Taberlet2012 protocol.…”

Section: Dna Extraction Methods For Sedadna Researchmentioning

confidence: 99%

“…The physical and chemical properties of sediments can have strong effects on the efficiency of DNA extraction from sediments. For instance, clay minerals and calcite both bind tightly to DNA [101,102,192] but require different extraction approaches to maximize DNA recovery. In the case study A6, we show that carbonate-rich sediments yield lower amounts of sedaDNA than organic-rich sediments using a conventional extraction protocol (PowerSoil kit) and an optimized extraction protocol can greatly improve vascular plant DNA recovery from carbonate-rich samples.…”

Section: Dna Extraction Methods For Sedadna Researchmentioning

confidence: 99%

“…Degradation and adsorption of DNA molecules at the water-sediment interface and in sediments: Environmental conditions in water and at the water-sediment interface and within the sediment column-such as temperature, redox state, conductivity and pHinfluence the rates and extent of both abiotic and biotic DNA degradation e.g., [66,67,100]. The adsorption of DNA to mineral particles was recently reported to be a strong factor controlling the persistence of DNA molecules in sedimentary archives [101,102]. Desorption of adsorbed DNA from the particulate phase in sediments can also occur and is dependent on the mineralogic composition, pore-water pH or the valence and concentrations of cations in the sediment [103].…”

Section: Influence Of Taphonomic Processes On the Burial And Persistementioning

confidence: 99%

“…If studying DNA from terrestrial organisms, it is important to first consider the size and topography of lake catchment and the hydrographic network to estimate the efficiency of DNA transfer to the lake following detailed recommendations from Giguet-Covex et al [39]. Sediment lithology (e.g., clay mineral content) may also impact the preservation potential of DNA in lake sediment [101], but further study is required to create a predictive framework for lithology-based site selection.…”

Section: Recommendationsmentioning

confidence: 99%

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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

et al. 2021

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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 on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

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Section: Dna Extraction Methods For Sedadna Researchmentioning

confidence: 99%

Section: Dna Extraction Methods For Sedadna Researchmentioning

confidence: 99%

Section: Influence Of Taphonomic Processes On the Burial And Persistementioning

confidence: 99%

Section: Recommendationsmentioning

confidence: 99%

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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

et al. 2021

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“…Finally, we highlight the importance of including additional geochemical measures, such as porewater chemistry 80 . and sedimentology 81 in future studies and measuring biomass by qPCR assay.…”

Section: Resultsmentioning

confidence: 99%

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

Moguel

Pérez

Alcaraz

et al. 2021

Sci Rep

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Metagenomic and traditional paleolimnological approaches are suitable to infer past biological and environmental changes, however, they are often applied independently, especially in tropical regions. We combined both approaches to investigate Holocene Prokaryote and Eukaryote diversity and microbial metabolic pathways in ancient Lake Chalco, Mexico. Here, we report on diversity among a large number of lineages (36,722 OTUs) and functional diversity (27,636,243 non-clustered predicted proteins, and 6,144 annotated protein-family genes). The most abundant domain is Bacteria (81%), followed by Archaea (15%) and Eukarya (3%). We also determined the diversity of protein families and their relationship to metabolic pathways. The early Holocene (> 11,000 cal years BP) lake was characterized by cool, freshwater conditions, which later became warmer and hyposaline (11,000–6,000 cal years BP). We found high abundances of cyanobacteria, and fungi groups associated with mature forests in these sediments. Bacteria and Archaea include mainly anaerobes and extremophiles that are involved in the sulfur, nitrogen, and carbon cycles. We found evidence for early human impacts, including landscape modifications and lake eutrophication, which began ~ 6,000 cal years BP. Subsaline, temperate conditions were inferred for the past 5,000 years. Finally, we found nitrogen-fixing bacteria and protein-family genes that are linked to contaminated environments, as well as several fungal pathogens of crops in near-surface sediments.

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Preservation of sedimentary plant DNA is related to lake water chemistry

et al. 2021

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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.

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Geochemical identification of potential DNA-hotspots and DNA-infrared fingerprints in lake sediments

Cited by 27 publications

References 46 publications

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico

Preservation of sedimentary plant DNA is related to lake water chemistry

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