Newly designed foraminifera primers identify habitat-specific lineages through metabarcoding analyses

Area of Science:

• Microbiology
• Ecology
• Evolutionary Biology

Background:

• Foraminifera are diverse, shell-building protists inhabiting various aquatic environments.
• They serve as crucial bioindicators for environmental changes.
• Comparative studies on foraminiferal biodiversity across major habitats using molecular tools are limited.

Purpose of the Study:

• To conduct a comparative analysis of foraminiferal biodiversity across freshwater, brackish, intertidal, and marine ecosystems.
• To develop and test new foraminifera-specific primers for SSU-rRNA gene metabarcoding.
• To explore the diversity of foraminifera, particularly in understudied freshwater habitats.

Main Methods:

• Development of novel foraminifera-specific primers targeting the SSU-rRNA gene.
• Metabarcoding survey of foraminiferal communities in intertidal, coastal, and freshwater vernal pool ecosystems.
• Analysis of operational taxonomic units (OTUs) and their habitat preferences.

Main Results:

• A total of 655 operational taxonomic units (OTUs) were identified, with many being previously undetermined taxa.
• 163 OTUs exhibited distinct habitat preferences.
• Single-chambered foraminifera, including Reticulomyxa-like forms from freshwater, dominated the observed OTUs.

Conclusions:

• The study provides new molecular tools for foraminiferal diversity research.
• Significant unexplored foraminiferal diversity exists across different aquatic habitats.
• Freshwater foraminifera represent a poorly understood but diverse group requiring further investigation.