Open AccessA practical introduction to microbial molecular ecology through the use of isolation chips
Author(s) -
Alessi Anna M.,
Redeker Kelly R.,
Chong James P. J.
Publication year - 2018
Publication title -
ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.17
H-Index - 63
ISSN - 2045-7758
DOI - 10.1002/ece3.4748
Subject(s) - context (archaeology) , isolation (microbiology) , microbial ecology , ecology , species richness , biology , amplicon sequencing , molecular ecology , metagenomics , amplicon , 16s ribosomal rna , rarefaction (ecology) , data science , computational biology , computer science , bioinformatics , bacteria , genetics , sociology , gene , polymerase chain reaction , paleontology , population , demography
In the context of antimicrobial 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 4 year undergraduate Masters Program, 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 coordinate analyses to the interpretation of the data they obtained from high throughput sequencing. Our results confirmed that isolation chips 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.