Microbial interactions in soil

In the previous chapters, we have seen that soil generally offers quite varied and fluctuating conditions to its inhabitants. Due to the heterogeneous nature of soil, the occurrence of spatial and temporal gradients of many compounds of quite different nature, be they in the gaseous or liquid phases, is the rule rather than the exception. Hence, the microbes that have successfully adapted to soil must have developed specific “skills” to cope with all of its vagaries. A key aspect that determines the fitness of microorganisms in soil is obviously the capacity of the microbial cells to interact appropriately with their immediate abiotic and/or biotic environments. In addition to the physiological adaptation strategies of microbial cells (discussed in Chapter 4), soil microorganisms must have evolved strategies that allow them to sense, and interact with, their immediate surroundings, in order to “fine-tune” their cellular metabolism to locally-determined conditions. The basic conjecture here is this environmental sensing is based on the perception of a range of chemical compounds in soil, and, in this respect, it is irrelevant whether the environmental stimuli are abiotic or biotic in origin. In fact, most environmental sensing is based on the perception of gradients in the concentrations of specific compounds, whether these are of abiotic (e.g. specific substrates that may serve as nutrients, volatiles, protons) or biotic (e.g. signaling compounds) origin. Here, we will discuss the interactions of microorganisms in their microhabitats in soil, in particular in relation to other microorganisms that are present. The focus will be on the molecular mechanisms that are used in the perception of the neigh- boring organisms, and the strategies employed to communicate with them, i.e. by sending out and/or receiving signals of different kinds.