Molecular Community Indices

Bio-monitoring

Bio-monitoring is essential to help us understand and maintain the health of our ecosystems. Bio-monitoring of aquatic systems is done by studying the communities that live in these environments. These communities provide a way to monitor long-term river health. Current bio-monitoring uses microscope analysis to identify and classify the invertebrates that live in the community. This requires a high degree of taxonomic expertise and can result in high costs/slow turn-around times.

We looked at ways to develop a molecular approach to evaluating these macroinvertebrate communities. We tested two methods for examining the communities. The first was a more traditional amplicon sequencing approach (comparable to 16S sequencing of microbial communities). The second used a gene enrichment approach in which DNA was fragmented and captured by sequence probes.

geneEnrichvsPCR

We could show that the gene enrichment approach worked far better than a traditional amplicon sequencing for evaluating macroinvertebrate communities. The amplicon sequencing struggled with priming bias (despite degenerate primers) and often missed taxa altogether. The gene enrichment approach generated per taxa sequence counts proportional to the taxa biomass estimates generated before DNA extraction.

 

For more details see:

Dowle, E.J., X. Pochon, J. C. Banks, K. Shearer, and S.A. Wood, Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates. Molecular Ecology Resources, 2016. 16, 1240–1254

Dowle, E., X. Pochon, N. Keeley, and S.A. Wood, Assessing the effects of salmon farming seabed enrichment using bacterial community diversity and high throughput sequencing. FEMS Microbiology Ecology, 2015.