Dumpster diving for diatom plastid 16S rRNA genes.

Area of Science:

• Environmental microbiology
• Aquatic ecology
• Bioinformatics

Background:

• Diatoms are crucial primary producers in global aquatic ecosystems.
• Monitoring diatom communities is essential for assessing ecosystem health.
• High-throughput sequencing offers efficient methods for microbial community analysis.

Purpose of the Study:

• To evaluate the efficacy of the V4 515F-806RB primer pair for amplifying diatom plastid 16S rRNA sequences.
• To classify diatom operational taxonomic units (OTUs) in Australian freshwater biofilms using the PhytoREF database.
• To assess the utility of existing 16S rRNA amplicon datasets for diatom distribution studies.

Main Methods:

• Analysis of 72 freshwater biofilm samples from streams in south-eastern Australia.
• Classification of 16S rRNA reads using the PhytoREF database and filtering for Bacillariophyta (diatoms).
• Comparison of diatom OTUs with publicly available 16S rRNA datasets from the NCBI-SRA database.

Main Results:

• The 515F-806RB primer pair successfully amplified diatom plastid 16S rRNA sequences.
• PhytoREF classification identified 71 diatom OTUs, representing over 90% of diatom reads in samples.
• Beta-diversity analyses revealed significant differences in diatom assemblages among river segments.
• 67 out of 71 identified diatom OTUs were detected in other Australian 16S rRNA datasets.

Conclusions:

• Standard V4 515F-806RB primers are effective for recovering diatom 16S rRNA sequences.
• Existing 16S rRNA amplicon data can be repurposed for diatom detection, characterization, and distribution mapping.
• This approach supports ecological health assessments and has potential for broader ecological and industrial applications.