Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation

Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models

Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).1.

Exposure to polystyrene nanoplastics reduces bacterial and fungal biomass in microfabricated soil models

Nanoplastics have been proven to induce toxicity in diverse organisms, yet their effect on soil microbes like bacteria and fungi remains largely unexplored. In this paper, we used micro-engineered soil models to investigate the effect of polystyrene (PS) nanospheres on Pseudomonas putida and Coprinopsis cinerea. Specifically, we explored the effects of increasing concentrations of 60 nm carboxylated bovine serum albumin (BSA) coated nanospheres (0, 0.5, 2, and 10 mg/L) on these bacterial and fungal model organisms respectively, over time. We found that both microorganisms could disperse through the PS solution, but long-distance dispersal was reduced by high concentrations. Microbial biomass decreased in all treatments, in which bacteria showed a linear dose response with the strongest effect at 10 mg/L concentration, and fungi showed a non-linear response with the strongest effect at 2 mg/L concentration. At the highest nanoplastics concentration, the first colonizing fungal hyphae adsorbed most of the PS nanospheres present in their vicinity, in a process that we termed the 'vacuum cleaner effect'. As a result, the toxicity effect of the original treatment on subsequently growing fungal hyphae was reduced to a growth level indistinguishable from the control. We did not find evidence that nanoplastics are able to penetrate bacterial nor fungal cell walls. Overall, our findings provide evidence that nanoplastics can cause a direct negative effect on soil microbes and highlight the need for further studies that can explain how the microbial stress response might affect soil functions.

Habitat complexity affects microbial growth in fractal maze

The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers' point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.