The driving role of microhabitats in soil ecology: rebuilding artificial 3D soil-like nanostructured microhabitats for experimental reproducible works

Soil ecosystems are composed of microhabitats that often differ in composition and ecological strategies at the microscale. Besides, the assumption that soil organism behaviour at the ecosystem level is similar to that at microscale may drive unexpected findings. Soil pH at microsites either can differ significantly from whole soil pH. Moreover, the large porosity measured in the whole soil can contrast with water, nutrient, air and waste flow limitations and dramatic constraints to microbial mobility and access to food, when analysed at the microscale, consequent to local pore geometry, connectivity and tortuosity. Incidentally, soil microorganisms, which are present in billions of individuals per gram of soil, have micrometre sizes and prevalently interact with the other soil components at the nano-to-microscale. They colonise soil microhabitat based on the local concentration and composition of air, nutrients and materials. Finally, different organic materials and minerals in the soil induce distinct interactions at microsites, generating diverse organo-mineral associations and different microbial populations. 

The study of soil microhabitats can enable comprehending how the microsites' dynamics can drive to ecosystems' macroscale behaviours. However, the study of soil microhabitats in real conditions, even when investigated in soil mesocosms and microcosms, can be challenging or require complicated and expensive instrumentations to achieve such outcomes. 

The rebuilding of soil microhabitats in model systems can help study the microhabitats' mutual interactions at the microscale. However, it is impossible to reproduce any possible combination of soil components to replicate the multitude of microhabitats existing in natural soil ecosystems. Then, approximations are necessary. 

The present study proposes to recreate an artificial model 3D soil-like microhabitat resulting from the aggregation of the major classes of soil components (mineral particles, organic polymeric components, and microorganisms) in nano- to macro-architectures to study organo-mineral-microbe interactions at the microscale, and enable reproducible works. Electrospinning/electrospraying technologies were chosen for their extreme versatility in creating self-standing 3D complex, porous and functional structures and their proven capacity to permit microbes to grow on the resulting composite fibrous frameworks.

Bacteria strains of Pseudomonas fluorescens and Burkholderia terricola, typical microbial species populating the rhizosphere soils, will be utilised as microhabitat microbial components for generating a simplified microbiome in the 3D soil-like nanostructures. At first instance, we intended to use microscopy (e.g. SEM, TEM, confocal) as the tool of choice to investigate over time the spatial distribution of bacterial populations throughout the artificial nanostructured soil microhabitat here reproduced, the release of EPS by the bacterial populations and possible interactions. The proposed 3D soil-like nanostructures are supposed to provide the possibility of investigating the microbial lifestyle in microhabitats at different scales, from nm to mm, then linking microbial phenotypic traits to specific soil features.