DNA Metabarcoding Uncovers Hidden Diversity in Stream Invertebrate Communities

Wed, 17, May, 2023 by Food from Thought

Researchers from the University of Guelph have discovered high levels of hidden diversity in benthic invertebrate communities (invertebrates that live on the bottom of streams and rivers and are visible to the naked eye) using DNA metabarcoding.

The Food from Thought-funded study, led by former Phd student Dr. Jennifer Gleason and co-advised by Drs. Karl Cottenie and Robert Hanner, was published recently in the BMC Ecology and Evolution Journal, and highlights the importance of incorporating molecular identification techniques, specifically DNA metabarcoding, into biomonitoring programs to understand local biodiversity better.

Freshwater ecosystems, particularly streams, are under increasing pressure from agricultural land use and climate change. Detecting global trends in insect decline is crucial for assessing ecological conditions. Aquatic insects and other tiny organisms are commonly used as indicators of freshwater ecosystem health. However, their diverse nature poses challenges for accurate morphological identification, and relying on coarse taxonomic resolution can obscure patterns in community composition.

The researchers aimed to explore the diversity and variability of aquatic macroinvertebrate communities at small spatial scales by integrating DNA metabarcoding into a stream biomonitoring sampling design. They sampled twenty streams in southern Ontario at multiple time points, comparing field replicates taken ten meters apart within the same stream.

Using bulk-tissue DNA metabarcoding, the researchers unveiled the highly diverse nature of aquatic macroinvertebrate communities at small spatial scales, revealing unprecedented levels of local taxonomic turnover. They detected over 1600 Operational Taxonomic Units (OTUs) from 149 families. Interestingly, the Chironomidae family, a type of non-biting midges, accounted for more than a third of the total number of OTUs detected. The benthic communities were predominantly composed of rare taxa, with many detected only once per stream despite multiple biological replicates.

The study also highlighted that a significant proportion of taxa remained undetected by the sampling regime, emphasizing the need for improved sampling protocols. The sites were located across a gradient of agricultural activity, but contrary to expectations, increased land use did not homogenize benthic communities. The within-stream dissimilarity, a measure of community composition variation, remained consistently high at all levels of taxonomic resolution, indicating that stream communities differ significantly at small spatial scales.

“As climate change intensifies and the decline of insect populations raises concerns, conserving vulnerable habitats and slowing biodiversity loss becomes critical,” said Gleason.

“Insect decline has been well-documented, and freshwater habitats, including streams, are particularly at risk. Biomonitoring programs often rely on aquatic invertebrates as bioindicators, but the limitations of morphological identification calls for more efficient methods.”

She says molecular tools, such as DNA metabarcoding, offer promising solutions for assessing freshwater biodiversity. Previous studies comparing morphological identification with DNA metabarcoding have demonstrated the effectiveness of molecular methods in investigating biodiversity patterns. High-throughput sequencing platforms can efficiently sequence and identify entire samples, providing valuable insights for environmental assessments.

The study’s findings contribute to developing improved biomonitoring protocols and efficiently recording biodiversity in stream systems. By incorporating DNA metabarcoding, researchers can overcome the challenges of small-scale stream habitat variations and better understand local community composition.

Understanding the dynamics of benthic invertebrate communities at small spatial scales is crucial for effective conservation and management of freshwater ecosystems. The study highlights the importance of considering hidden diversity and variability when assessing the health of stream ecosystems and emphasizes the value of molecular tools in biomonitoring efforts.

Read the research study here