Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil

Abstract

Aims: One of the main challenges of culture-independent soil microbiology is distinguishing the microbial community’s viable fraction from dead matter. Propidium monoazide (PMA) binds the DNA of dead cells, preventing its amplification. This dye could represent a robust means to overcome the drawbacks of other selective methods, such as ribonucleic acid-based analyses. Methods and results: We quantified functional genes from viable archaea and bacteria in soil by combining the use of PMA and quantitative polymerase chain reaction. Four N-cycle-related functional genes (bacterial and archaeal ammonia monooxygenase, nitrate reductase, and nitrite reductase) were successfully quantified from the living fraction of bacteria and archaea of a paddy soil. The protocol was also tested with pure bacterial cultures and soils with different physical and chemical properties. Conclusions: The experiment results revealed a contrasting impact of mineral and organic fertilizers on the abundance of microbial genes related to the N-cycle in paddy soil. Significance and impact of study Data obtained on the same samples only by quantitative polymerase chain reaction, without using propidium monoazide, did not show differences in treatments, suggesting that this dye can highlight the active fraction of microorganisms, adding sensitivity to the study of essential soil functions.