How do rhizosphere bacteria interact with their environment at the microhabitat scale?

Abstract

The rhizosphere supports greater bacterial densities than root-free soil. Rhizosphere bacteria (RB) can affect plant health and nutrition however, attempts to manipulate introduced and/or indigenous communities to benefit plants are unreliable. Current evidence indicates that habitat factors strongly influence bacterial communities. In the rhizosphere many processes give rise to a high degree of habitat heterogeneity therefore, to understand how RB interact with their environment their ecology should be studied at the micro-spatial-scale. The objectives of this research were to develop a method for sampling RB at the microhabitat-scale, and to investigate techniques that can link these samples with key factors, such as substrate availability and pH. A novel method enabling non-destructive, micro-scale sampling of bacteria was developed. Its efficiency for removing bacteria from the root surface was similar to that of existing methods but offered greater accuracy in estimating RB densities. The novel method revealed that RB density was inversely proportional to distance from the apex of Brassica napus roots and that the composition of RB communities was highly variable at the micro-scale. Imaging of 14C-labelled root exudates revealed that RB density was not reflective of exudate availability but attempts to link RB with available C were unsuccessful. A key outcome of this work was the development of a strategy to combine micro sampling with microelectrode measurements. Microelectrodes revealed that pH at the root surface was highly variable at the micro-scale which, combined with similar observations for RB density/diversity, highlights the appropriateness of this scale for linking RB communities with their environment. This thesis considers the link between RB community structure, habitat and function and provides a detailed description of micro-sample analyses as well as a set of methods that will enable for the first time, the interactions between any surface-associated bacteria and their environment to be investigated at a microhabitat-scale