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How do fungi navigate through the complex microscopic maze-like structures found in the soil? Fungal behaviour, especially at the hyphal scale, is largely unknown and challenging to study in natural habitats such as the opaque soil matrix. We monitored hyphal growth behaviour and strategies of seven Basidiomycete litter decomposing species in a micro-fabricated “Soil Chip” system that simulates principal aspects of the soil pore space and its micro-spatial heterogeneity. The hyphae were faced with micrometre constrictions, sharp turns and protruding obstacles, and the species examined were found to have profoundly different responses in terms of foraging range and persistence, spatial exploration and ability to pass obstacles. Hyphal behaviour was not predictable solely based on ecological assumptions, and our results obtained a level of trait information at the hyphal scale that cannot be fully explained using classical concepts of space exploration and exploitation such as the phalanx/guerrilla strategies. Instead, we propose a multivariate trait analysis, acknowledging the complex trade-offs and microscale strategies that fungal mycelia exhibit. Our results provide novel insights about hyphal behaviour, as well as an additional understanding of fungal habitat colonisation, their foraging strategies and niche partitioning in the soil environment.

How do fungi navigate through the complex microscopic maze-like structures found in the soil? Fungal behaviour, especially at the hyphal scale, is largely unknown and challenging to study in natural habitats such as the opaque soil matrix. We monitored hyphal growth behaviour and strategies of seven Basidiomycete litter decomposing species in a micro-fabricated “Soil Chip” system that simulates principal aspects of the soil pore space and its micro-spatial heterogeneity. The hyphae were faced with micrometre constrictions, sharp turns and protruding obstacles, and the species examined were found to have profoundly different responses in terms of foraging range and persistence, spatial exploration and ability to pass obstacles. Hyphal behaviour was not predictable solely based on ecological assumptions, and our results obtained a level of trait information at the hyphal scale that cannot be fully explained using classical concepts of space exploration and exploitation such as the phalanx/guerrilla strategies. Instead, we propose a multivariate trait analysis, acknowledging the complex trade-offs and microscale strategies that fungal mycelia exhibit. Our results provide novel insights about hyphal behaviour, as well as an additional understanding of fungal habitat colonisation, their foraging strategies and niche partitioning in the soil environment.

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 putidaand 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.

Zinc (Zn) is an important trace element that is essential for optimal plant growth. Zinc-solubilising bacteria can release Zn from its insoluble compounds. We isolated and identified Zn-solubilising bacteria (ZnSB) from the rhizosphere, and semi-quantitively and quantitatively evaluated their ability to dissolve various Zn minerals (ZnO, ZnCO3and Zn3(PO4)2). Out of 24 rhizosphere soil samples, 15 strains of Zn-solubilising bacteria were isolated and purified. Five isolates that were found to be the most efficient in solubilising insoluble Zn compounds were identified based on gene 16S rRNA sequencing. Three of the isolates belonged to the genus of Pseudomonas, and two to Enterobacter. The highest solubilisation index among the three insoluble Zn compounds was observed in Pseudomonas putida(3.31) in the culture medium containing ZnO. Among the three tested insoluble compounds, the highest mean solubility by the strains was obtained from ZnO, followed by ZnCO3, and Zn3(PO4)2, respectively. The highest rate of Zn release among the three insoluble compounds was obtained in the culture medium of the Pseudomonas fluorescencestrain Ur22 (35.6 mg L−1), which was ten times as great as that of the background solubilisation observed in the sterile control culture medium (3.8 mg L−1). Zn solubilisation was associated with a strong pH decrease in the culture medium, the strongest for Pseudomonas fluorescence(Ur21), which lowered pH to 4.2 compared to the control at pH 6.8. We concluded that the identification of effective ZnSB, and their use as bio-fertiliser, will help improve plant nutrition and production.

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.