Visualizing and identifying selfish bacteria: a hunting guide

Abstract

Polysaccharides are dominant components of plant biomass, whose degradation is typically mediated by heterotrophic bacteria. These bacteria use extracellular enzymes to hydrolyze polysaccharides to oligosaccharides that are then also available to other bacteria. Recently, a new mechanism of polysaccharide processing - selfish uptake - has been recognized, initially among gut-derived bacteria. In selfish uptake, polysaccharides are bound at the outer membrane, partially hydrolyzed, and transported into the periplasmic space without loss of hydrolysis products, thus limiting the availability of smaller sugars to the surrounding environment. Selfish uptake is widespread in environments ranging from the oceans cool, oxygen-rich, organic carbon-poor waters to the warm, carbon-rich, anoxic environment of the human gut. We provide a detailed guide of how to hunt for selfish bacteria, including how to rapidly visualize selfish uptake in complex bacterial communities, identify selfish organisms, and distinguish the activity of selfish organisms from other members of the community.