Microbial Community Dynamics in Soil

It is now well-understood that microbiome plays a critical role in determining the health status of its animal host or any environmental ecosystem. In plants too, it is now becoming clear that the microbiome governs overall health of the pod. The first interaction between plant and microbes happen in soil. Further, each plant is associated with a unique rhizosphere microbial community, members of which have been selected from a plethora of microbes present in the soil. Evidently, the interactions between the three components: plants, microbes and soil system play a critical role in this establishment. However, the complexity of these interactions is not yet clear. It is this tri-partite interaction between plant-microbe-soil that my research program aims to decipher. At the same time, these interactions cannot be partitioned into components and must be studied concomitantly to better understand the real- scenario as it happens, preferably in their most pristine conditions.

Long-term succession of microbial communities in bulk soil is ecosystem dependent (Deonalli et al. 2017). In sand dunes, communities undergo continuous maintenance (overlap) accompanied by a concomitant replacement (turnover) during 77,000 years of ecosystem development or as the soil ages (Tarlera et al., 2008). While microbial diversity increases with soil developmental age during natural succession, it has a non-linear correlation with the intensity of disturbance in agricultural soils (Jangid et al., 2008). Upon restoration of disturbed soils, transitional microbial communities are formed that differ significantly from those in disturbed and native soils (Jangid et al., 2010). In fact, land-use history has a stronger impact on soil microbial communities than aboveground vegetation or soil properties (Jangid et al., 2011). Further, research from glacial retreats in New Zealand suggests that succession of microbial communities is closely aligned with ecosystem development, pedogenesis and vegetative succession (Jangid et al., 2013a and 2013b). Whether this ecosystem dependence in bulk soils is also reflected in the selection of rhizosphere microbial communities?

Fig. 4.1

Fig. Microbial community succession across different ecosystems (Deonalli et al. 2017). Different natural and human-induced events lead to the creation of “near-pristine” ecosystems on which primary succession proceeds. Among the first colonizers of such “bare” ecosystems are the microbial communities that develop concomitantly with the development of the ecosystem. At the same time, the interactions with the abiotic and biotic factors directly impact the development of microbial communities that are responsible for many functions within the ecosystem for it to develop further. During such successional events, many changes take place within the ecosystem, e.g., the early stages primarily dominated by bacteria and late stages characterized by fungal dominance. However, there is an intermediate stage during this transition which significantly differs from the other two.

Impact craters are unique ecosystems, excellent for the study of plant-microbe-soil interactions in its most pristine form (see the Earth Impact Database for known Craters). Often the intense heat and pressures reached at the point of contact create sterile conditions at the immediate area of the impact. Such sites usually contain very different ecosystems from those that surround them sharing a high degree of similarity with other primary succession habitats (habitats that are completely bare for recolonization), such as high intensity fires and volcanism. The information on the microbial community succession at impact craters is very limited and opens a new avenue to explore how microbes interact with the aboveground vegetation during initial stages of establishment.

It is hypothesized that the core component of the complex interactions between plant-microbes in agricultural soils will be a reflection of those in pristine soils. Hence, the information gleaned from such sites on community succession and interactions would be instrumental in devising strategies to improve overall plant health. Using omics approaches, we are now investigating these direct interactions in greater depths.