Does filter pore size introduce bias in DNA sequence-based plankton community studies?

Area of Science:

• Microbial Ecology
• Molecular Biology
• Limnology

Background:

• Microbial eukaryotic plankton (0.2–200 μm) are crucial to aquatic ecosystems.
• High-throughput sequencing revolutionizes plankton studies.
• The accuracy of size-fractionated environmental DNA (eDNA) methods for microbial eukaryotes is uncertain.

Purpose of the Study:

• To assess the accuracy and effectiveness of size-fractionated filtration combined with eDNA methods for microbial eukaryotic plankton.
• To compare one-step (0.2–200 μm) and size-fractionated (0.2–3 μm and 3–200 μm) filtration strategies.
• To understand the influence of filtration bias on microbial eukaryotic community composition.

Main Methods:

• Collected water samples from two subtropical reservoirs.
• Applied two filtration strategies: one-step (0.2–200 μm) and size-fractionated (0.2–3 μm and 3–200 μm).
• Analyzed microbial eukaryotic communities using 18S rRNA gene sequencing and quantified gene copy abundance.

Main Results:

• 18S rRNA gene copy abundance differed by less than 50% between filtration methods for most samples.
• Despite similar gene copy numbers, significant differences in community composition were observed between the 0.2–200 μm and the combined 0.2–3 μm and 3–200 μm fractions.
• Size-fractionation bias disproportionately affected unique operational taxonomic units (OTUs) and low-abundance OTUs, particularly in specific seasons.

Conclusions:

• Size-fractionated filtration provides a comparable gene copy abundance to one-step filtration for microbial eukaryotes.
• Filtration strategy significantly impacts the perceived community composition, especially for rare taxa.
• These findings offer critical insights for optimizing molecular methods in microbial eukaryote research.