Metagenomics of dormancy and implications for the maintenance of microbial diversity

Background/Question/Methods

Dormancy is a bet-hedging strategy used by a wide range of taxa, including microorganisms. It refers to an organism’s ability to enter a reversible state of low metabolic activity when faced with unfavorable environmental conditions. Importantly, dormant microorganisms generate a seed bank, which comprises individuals that are capable of being resuscitated following environmental change. Thus, microbial dormancy may help maintain biodiversity and influence the stability of ecosystem processes.  In the first part of the talk, we will present results from a meta-analysis on the prevalence of dormancy in a variety of ecosystems, including oceans, lakes, soils, and the human gut.  In the second part of the talk, we will present results on the role that communication signaling plays in the regulation of dormancy.  Specifically, we will focus on resuscitation promoting factor (Rpf), a protein produced by some soil bacteria (e.g., Actinobacteria) that is responsible for the transition of cells from a dormant to active state.  

Results/Conclusions

Our meta-analysis suggests that dormancy is prevalent in a variety of natural and managed ecosystems.  For example, up to 90% of the bacterial cells in soil environments are inactive, and approximately 50% of all bacterial “species” can be considered dormant.  Metagenomics analysis revealed that the mechanisms of dormancy in clinically important bacteria are also present in environmental samples.  For example, toxin-antitoxin modules that are known to regulate dormancy in E. coli could be found in the human gut and in activated sludge.  Last, our metagenomic analysis revealed that genes encoding for resuscitation promoting factors (rpf) can be found in approximately 25% of the bacterial genomes in soils.  This observation led us to screen rpf genes in a collection of soil isolates.  We were able to clone, express, and purify Rpf from a population of Micrococcus. Preliminary results indicate that Rpf may play an important direct and indirect role in the maintenance of diversity and function in microbial communities.