Culturable diversity of Bacteria and Archaea
Microbes from the domain Archaea and Bacteria inhabit almost every known ecosystem on earth and are expected to be a likely life form in other planets.
Reflecting their large distribution in variable conditions and settings, Archaea and Bacteria hold a wide diversity of members across deep (i.e. phyla) to shallow (i.e. populations) levels of phylogeny (relatedness). Despite of their high diversity and abundance a very small number of these microbes are successfully grown in the lab. Isolating organisms and their study under controlled conditions has multiple benefits including understanding and measuring the physiological activity of microbes, being able to test microbes for evolutionary processes, evaluating mechanisms of resistance to environmental stress, screening for biotechnological application, measurement of kinetics for higher level ecosystem models, and much much more.
Our efforts in this research focus on testing cultivability factors for heterotrophic bacteria and methanogenic Archaea. One of the main variables under evaluation includes preconditioning inoculums to “activate” numerically dominant yet rarely cultured microbes; another strategy deal with using biochemical additions targeted to reduce environmental stress to microbes. These novel approaches are done in conjunction with other well-established approaches including substrate manipulations, in some cases natural pre enrichments, and physical separation of cells.
One of the most unique aspects of this work is that most of this research is conceived, executed and evaluated by undergraduate researchers in the MENTOR@ASU program (see facebook page). In 2012-2013, in collaboration with Dr. Ferran Garcia-Pichel at ASU and Dr. Eoin Brodie at Lawrence Berkeley National Lab, a collection of nearly 700 heterotrophic isolates from dessert crust soils have been developed. Novel species are being evaluated for publication, a set of 15 genomes is being sequenced, and experiments reconstructing metabolic networks are under development (in collaboration with Dr. Trent Northern at LBNL) using the isolates from the undergraduates work. Also, the group of students is highly active recruiting and training female and minority students in science, and offers an opportunity for educational collaboration with institutions with more limited access to undergraduate students such as national laboratories and institutes.
Roseomonadales strain (new species) in characterization by E. Hummel. From left to right: early colonies at 14 days (10x), late “columnar” colonies (45X), cell aggregated as microcolonies (100X). Importantly this cell only grows as aggregates and no planktonic growth has been seen so far.