Innovative Technologies Can Improve Understanding of Microbial Nitrogen Dynamics in Agricultural Soils

Abstract

Roughly half of all nitrogen (N) added to soils is not incorporated by crops and is lost to the environment, but our ability to reduce N loss from soils is hampered by an inadequate grasp of microbial processes affecting N retention and mobility. High-throughput sequencing (HTS) of microbial DNA is enabling fundamental insights into N cycling microorganisms and their metabolisms. This commentary describes six emerging technologies that could be combined with HTS to enable real-time collection of metadata on N transformations, intermediates, and products to link soil properties, microbial processes, and the fate of N. These technologies include microdialysis and microfluidics, automated sensing, microfabrication of model soils, parallel quantification of N functional genes, sorting active cells, and stable isotope probing. Use of integrated technologies applied initially under controlled conditions at small scales can lead to identification of soil conditions and field-scale management practices that promote better N conservation and delivery to agricultural crops.

Combined Use of Vinasse and Nitrogen as Fertilizers Affects Nitrification, Ammonification, and Denitrification by Prokaryotes

“…Cloutier et al (25) described the parallel quantification of N functional genes as one emerging technology that could be combined with high-throughput sequencing of microbial DNA to study N metabolism in soil. The microarray technology GeoChip v.5.0M (Agilent Technologies Inc., Santa Clara, CA, United States) has become a powerful and high-performance tool to monitor environmental processes with high-sensitivity detection of microbial functional genes (26)(27)(28)(29).…”

Multianalytical approach in the study of the composition and functionality of the microbiota associated with carbon and nitrogen cycles in soils under preserved and disturbed environments

“…Genes nifH (N fixation), amoA (N nitrification), norB/C, and nirK/S (N denitrification) have been proposed for evaluating N cycling functions in soil (ANAND, 2012;PROSSER, 2012;PHILLIPOT, 2002). These genes can be monitored by molecular techniques such as microarray, real time quantitative polymerase chain reaction (RT-qPCR), high-throughput sequencing, and emerging technologies (SCHLOTER et al, 2018;CLOUTIER et al, 2019) to better understand physiological mechanisms in soil microbiota (LEHTOVIRTA-MORLEY, 2018).…”

“…However, experts warn about the imminent need to associate genomic data from molecular methods in Microbial Ecology with biochemical data, to close the "gap" between physiological mechanisms by AOA and N metabolism (Lehtovirta-Morley, 2018). Cloutier et al (2019) described the parallel quantification of N functional genes such as one emerging technology that could be combined with high-throughput-sequencing (HTS) of microbial DNA to study N metabolism in soil. The microarray technology GeoChip v.5.0M (Agilent Technologies Inc., Santa Clara, CA, United States) has become a powerful and highperformance tool to monitor environmental processes with high-sensitivity detection of microbial functional genes (Varon-Lopez et al, 2014;Shi et al, 2019;Zhao et al, 2020).…”