Open AccessTemperature-gradient incubation isolates multiple competitive species from a single environmental sample
Author(s) -
Karen M. Houghton,
Lucy C. Stewart
Publication year - 2020
Publication title -
access microbiology
Language(s) - English
Resource type - Journals
ISSN - 2516-8290
DOI - 10.1099/acmi.0.000081
Subject(s) - axenic , biology , amplicon , amplicon sequencing , 16s ribosomal rna , incubation , ecological niche , microbial ecology , bacteria , computational biology , ecology , microbiology and biotechnology , gene , genetics , polymerase chain reaction , biochemistry , habitat
High-throughput sequencing has allowed culture-independent investigation into a wide variety of microbiomes, but sequencing studies still require axenic culture experiments to determine ecological roles, confirm functional predictions and identify useful compounds and pathways. We have developed a new method for culturing and isolating multiple microbial species with overlapping ecological niches from a single environmental sample, using temperature-gradient incubation. This method was more effective than standard serial dilution-to-extinction at isolating methanotrophic bacteria. It also highlighted discrepancies between culture-dependent and -independent techniques; 16S rRNA gene amplicon sequencing of the same sample did not accurately reflect cultivatable strains using this method. We propose that temperature-gradient incubation could be used to separate out and study previously ‘unculturable’ strains, which co-exist in both natural and artificial environments.