Microbiome of St. Lawrence estuary sediments

Sampling

The myxobacteria are a widely dispersed group of Gram-negative bacteria known for their elaborate fruiting bodies. Principally soil bacteria, they are key players in the breakdown and processing of organic compounds in terrestrial soils, acting as both primary cellulose degraders and bacterial predators. While easily cultivated from soil, isolation of myxobacteria from lakes, rivers and oceans is rare, and for many years it was thought that myxobacteria were incapable of surviving in aquatic environments. We recently conducted a metagenomics analysis of several sites in the Gulf of St. Lawrence, examining the bacteria found free-living in the water column and attached to suspended marine sediment. While sequences corresponding to myxobacteria were not prevalent in the water column, they were widely dispersed in the sediments, forming up to 3-4 % of the active bacterial community in some cases. To determine the role of myxobacteria in the St. Lawrence estuary ecosystem, and to isolate any therapeutically relevant natural products that they may produce, we will pinpoint samples rich in myxobacteria via metagenomics. This will allow us to see how myxobacterial species prevalence changes as we move from freshwater to saltwater sediments.

Method steps

1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1