Phage-based biocontrol of nitrification in agricultural soil

Introduction

Nitrogen fertilization boosts crop yields but is inefficient due to the rapid activity of nitrifying bacteria, which leads to the loss of useful nitrogen forms. This requires the use of large amounts of fertilizers, leading to environmental pollution from compounds like NO₃ and N₂O. Although chemical inhibitors can improve fertilization, their impact on the environment and human health remains uncertain. A new strategy involves the use of bacteriophages (phages) that specifically target nitrifying bacteria.

Methods

Bacteriophages were isolated from sewage samples. The inhibition of nitrifying activity was tested in AOB medium and soil to monitor nitrite production with a colorimetric assay. The increase in bacteriophage particles during infection was assessed with qPCR. Controls without the addition of bacteriophages or bacteria were included for in vitro and soil samples. The persistence of infectious bacteriophages was analyzed in water suspensions and soil under different pH levels (3, 5, 6, 7, 8) and temperatures (4, 15, 22, 37 ^◦C) over 6 months.

Results

We isolated a bacteriophage (FNF-1) capable of infecting four species of Nitrosomonas. FNF-1 inhibited bacterial growth, resulting in a reduction in nitrite formation in phage-treated samples, both in vitro and in the soil. Meanwhile, FNF-1 increased by 2-log₁₀ units within 48 hours. Infectious FNF-1 remained stable in water suspensions for 6 months at 4, 15, 22, and 37 ^◦C and at pHs 6, 7, and 8 but was inactivated when exposed to pHs 3 and 5. In soils, FNF-1 infectivity showed a 2-log₁₀ reduction over 6 months.

Conclusions

This study presents a novel approach using bacteriophages to eliminate nitrifying bacteria. Bacteriophages as biocontrol agents offer an effective and environmentally friendly alternative to inhibit nitrification while overcoming the limitations of chemical products. While their application shows potential for improving agricultural fertilization, further research is required to scale up and optimize a product.