A practical introduction to microbial molecular ecology through the use of iChips

Sampling

In the context of anti-microbial resistance as one of the most serious issues faced globally by health providers, we explored a practical introduction to molecular microbial ecology. We designed field work and practical experiments for third year members of a four year undergraduate Masters Programme in which the students employed traditional and novel isolation techniques to identify antimicrobial activities from soil dwelling microorganisms. Students gained experience in isolating DNA from complex microbial communities, amplifying 16S rRNA genes and applied richness / diversity indices as well as principal coordinates analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips (iChips) facilitate the growth of a greater diversity and different species subset from the complex soil microorganism community than traditional plate spreading techniques. However, rarefaction of 16S rRNA amplicon sequencing data showed that the majority of observed species in soil remain unculturable by current methods. Based on the written reports produced by the students carrying out the work, we concluded that the described protocols are robust and informative, that these activities provide a good practical introduction to the theories and practice of molecular ecology and can be easily deployed to groups of six or more students in a cost-effective manner.

Method steps

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