Investigating variability in microbial community composition in replicate environmental DNA samples down lake...

Area of Science:

• Paleolimnology
• Microbial Ecology
• Molecular Paleontology

Background:

• Lake sediments serve as archives of past biological communities and catchments.
• Traditional paleolimnology relies on fossil organisms; molecular methods are emerging.
• Understanding sample heterogeneity and DNA degradation is crucial for molecular paleolimnology.

Purpose of the Study:

• To investigate bacterial community heterogeneity within 1-cm depth slices of lake sediments.
• To assess the adequacy of replicate sampling for characterizing ancient bacterial diversity using 16S rRNA metabarcoding.
• To determine if a single sample is sufficient for paleolimnological studies focusing on broad community shifts.

Main Methods:

• Collection of sediment cores from three lakes with varying sediment compositions.
• Sampling at multiple depths representing approximately 1,200 years of deposition.
• 16S rRNA metabarcoding analysis on triplicate samples from each depth slice.

Main Results:

• Three replicate samples were insufficient to capture the full bacterial diversity in most depth slices.
• Shared Amplicon Sequence Variants (ASVs) constituted the majority of reads, indicating dominant community structure.
• Replicates generally clustered together, and a single sample adequately characterized dominant bacterial ASVs for broad shifts.

Conclusions:

• For paleolimnological studies focused on broad-scale community shifts, a single sediment sample is sufficient for 16S rRNA metabarcoding.
• This finding simplifies future research by reducing the need for extensive replication when identifying major changes in ancient microbial communities.
• Potential issues like sediment laminae orientation can influence community dissimilarity in older samples.