Using metatranscriptomics to estimate the diversity and composition of zooplankton communities

Area of Science:

• Marine Biology
• Ecology
• Molecular Biology

Background:

• DNA metabarcoding is widely used for zooplankton biomonitoring but suffers from biases.
• Environmental DNA (eDNA), NUMT pseudogenes, and primer mismatches can inflate diversity estimates.
• Existing PCR-based methods may miss abundant species due to technical limitations.

Purpose of the Study:

• To evaluate metatranscriptomics as a superior alternative to DNA metabarcoding for zooplankton community analysis.
• To compare the accuracy of metatranscriptomics with PCR-based (gDNA, cDNA) and morphology methods.
• To validate metatranscriptomics for reliable species diversity and composition assessments.

Main Methods:

• Comparison of metatranscriptomics with gDNA and cDNA metabarcoding, and morphological identification.
• Analysis of mock communities and field-collected zooplankton samples.
• Assessment of species richness, nucleotide diversity, and composition.

Main Results:

• gDNA metabarcoding overestimated species richness due to eDNA contamination and NUMT pseudogenes.
• PCR-based methods showed higher sequence variants and indels compared to cDNA, indicating pseudogene interference.
• Metatranscriptomics yielded species diversity and composition estimates closely matching morphological data.
• Metatranscriptomics demonstrated consistent results across replicates and enabled monitoring of temporal changes.

Conclusions:

• Metatranscriptomics provides a robust and accurate method for zooplankton community biomonitoring.
• This RNA-based approach overcomes limitations associated with DNA metabarcoding biases.
• Metatranscriptomics is a valuable tool for ecological research and biodiversity assessments.