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Andrea Manfredini, Eligio Malusà, Flavia Pinzari, Loredana Canfora, Quantification of nitrogen cycle functional genes from viable archaea and bacteria in paddy soil, Journal of Applied Microbiology, Volume 134, Issue 8, August 2023, lxad169, https://doi.org/10.1093/jambio/lxad169
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Abstract
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.
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.
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.