Data from: A practical introduction to microbial molecular ecology through the use of isolation chips

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.