Comparing DNA extraction protocols for freshwater prokaryotic communities: impacts on yield and microbial profiling
Abstract
DNA extraction from aquatic samples is a critical process that influences the quantity and purity of the DNA obtained. This can have profound effects on the accuracy of the community depiction. In this study, DNA extraction workflows of seven commercial kits (Qiagen: DNeasy PowerLyzer PowerSoil, DNeasy PowerSoil Pro, DNeasy PowerSoil, DNeasy PowerMax Soil; Macherey-Nagel: NucleoSpin Soil; Zymo: ZymoBIOMICS DNA; MP Biomedicals: FastDNA SPIN), along with several modifications of manufacturer's protocols focusing on the lysis and elution steps, were tested, accounting for a total of 18 different protocols. For each protocol, DNA yield (quantity, replicability and quality), richness and compositional reproducibility based on 16S rRNA gene sequencing, as well as processing time and cost were assessed. The standard protocols recommended by the manufacturer showed comparable DNA yield results. Shared ASVs between all protocols accounted for >90% of the reads and were mostly abundant ASVs, indicating consistent detection of dominant taxa across all protocols. Adding supplementary lysis and elution steps to the manufacturer's protocols yielded up to ~4× more DNA. However, total read counts and ASV richness were lower as total DNA increased. Manufacturer's protocols therefore showed higher values than their modified versions, although these effects were not significant on community composition. We conclude that the choice of a protocol is the balance between recovering sufficient DNA of good quality versus potential effects on downstream sequencing output (reads and ASVs).
Related
- Adaptation of microbialite-associated prokaryotic communities to natural and experimental anoxic conditions
- Modeling freshwater use for direct lithium extraction from geothermal brines in the Salton Sea
- Radiative Transfer Modelling of Ka-band Microwave Interactions with Snow-Covered Freshwater Ice: Implications for SWOT KaRIn Property Retrieval
- Water pCO2 and planktonic food web temporal variations and couplings in drainage ditches of organically managed freshwater wetlands
- Occurrence of antibacterials, antivirals, and anti-inflammatory pharmaceuticals for COVID-19 treatment as emerging contaminants in the Chinese freshwater environment before, during and after the pandemic: the need for dynamic eco-pharmacovigilance
BibTeX
@article{szylit2026comparing,
title = {{Comparing DNA extraction protocols for freshwater prokaryotic communities: impacts on yield and microbial profiling}},
author = {Arthur Szylit and Ludwig Jardillier and Maria-Cristina Ciobanu and Léa Cabrol and Maialen Barret and Urania Christaki},
journal = {Peer Community In Microbiology},
year = {2026},
month = sep,
doi = {10.24072/pci.microbiol.100303},
url = {https://hal.science/hal-05835617v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Comparing DNA extraction protocols for freshwater prokaryotic communities: impacts on yield and microbial profiling
AU - Arthur Szylit
AU - Ludwig Jardillier
AU - Maria-Cristina Ciobanu
AU - Léa Cabrol
AU - Maialen Barret
AU - Urania Christaki
PY - 2026
DA - 2026/09/18
JO - Peer Community In Microbiology
DO - 10.24072/pci.microbiol.100303
UR - https://hal.science/hal-05835617v1
AB - DNA extraction from aquatic samples is a critical process that influences the quantity and purity of the DNA obtained. This can have profound effects on the accuracy of the community depiction. In this study, DNA extraction workflows of seven commercial kits (Qiagen: DNeasy PowerLyzer PowerSoil, DNeasy PowerSoil Pro, DNeasy PowerSoil, DNeasy PowerMax Soil; Macherey-Nagel: NucleoSpin Soil; Zymo: ZymoBIOMICS DNA; MP Biomedicals: FastDNA SPIN), along with several modifications of manufacturer's protocols focusing on the lysis and elution steps, were tested, accounting for a total of 18 different protocols. For each protocol, DNA yield (quantity, replicability and quality), richness and compositional reproducibility based on 16S rRNA gene sequencing, as well as processing time and cost were assessed. The standard protocols recommended by the manufacturer showed comparable DNA yield results. Shared ASVs between all protocols accounted for >90% of the reads and were mostly abundant ASVs, indicating consistent detection of dominant taxa across all protocols. Adding supplementary lysis and elution steps to the manufacturer's protocols yielded up to ~4× more DNA. However, total read counts and ASV richness were lower as total DNA increased. Manufacturer's protocols therefore showed higher values than their modified versions, although these effects were not significant on community composition. We conclude that the choice of a protocol is the balance between recovering sufficient DNA of good quality versus potential effects on downstream sequencing output (reads and ASVs).
SN - 2999-9332
ER -