Development and testing of an 18S rRNA phylogenetic microarray for marine sediments

Area of Science:

• Marine Biology
• Molecular Ecology
• Environmental Science

Background:

• Routine monitoring of anthropogenic effects on benthic biodiversity is crucial.
• Molecular methods, especially microarrays targeting phylogenetic marker genes like 18S rRNA, offer efficient biodiversity assessment.
• Microarrays can detect numerous taxonomic groups simultaneously and integrate into automated pipelines.

Purpose of the Study:

• To develop and test a microarray for eukaryotic biodiversity assessment in marine sediments.
• To design probes targeting 18S rRNA Operational Taxonomic Units (OTUs) from marine sediment metabarcoding data.
• To evaluate the microarray's specificity, sensitivity, and quantitative potential.

Main Methods:

• Designed probes targeting eukaryotic 18S rRNA OTUs from marine sediment metabarcoding.
• Tested the microarray with a spiked sample of 50 plasmid-clones and genomic DNA from marine sediments.
• Developed a filtration pipeline to reduce noise and false positives for accurate OTU detection and quantification.

Main Results:

• The microarray successfully detected and quantified OTUs with ≥0.1% abundance in the spiked sample.
• Specificity was high at broader taxonomic levels but decreased for closely related OTUs due to cross-hybridization.
• A positive correlation between hybridization signals and sequencing read abundance indicated quantitative performance with genomic DNA.

Conclusions:

• Microarrays targeting 18S rRNA show promise as a tool for high-throughput monitoring of marine benthic biodiversity.
• The developed filtration pipeline enhances the reliability of microarray-based biodiversity assessments.
• Further optimization may improve specificity for closely related taxa, expanding the application of this technology.