Development of rapid and precise approach for quantification of bacterial taxa correlated with soil health

Abstract

The structure and dynamic of soil bacterial community play a crucial role in soil health and plant productivity. However, there is a gap in studying the un−/or reclaimed soil bacteriome and its impact on future plant performance. The 16S metagenomic analysis is expensive and utilize sophisticated pipelines, making it unfavorable for researchers. Here, we aim to perform (1) in silico and in vitro validation of taxon-specific qPCR primer-panel in the detection of the beneficial soil bacterial community, to ensure its specificity and precision, and (2) multidimensional analysis of three soils/locations in Egypt (‘Q’, ‘B’, and ‘G’ soils) in terms of their physicochemical properties, bacteriome composition, and wheat productivity as a model crop. The in silico results disclosed that almost all tested primers showed high specificity and precision toward the target taxa. Among 17 measured soil properties, the electrical conductivity (EC) value (up to 5 dS/m) of ‘Q’ soil provided an efficient indicator for soil health among the tested soils. The 16S NGS analysis showed that the soil bacteriome significantly drives future plant performance, especially the abundance of Proteobacteria and Actinobacteria as key indicators. The functional prediction analysis results disclosed a high percentage of N-fixing bacterial taxa in ‘Q’ soil compared to other soils, which reflects their positive impact on wheat productivity. The taxon-specific qPCR primer-panel results revealed a precise quantification of the targeted taxa compared to the 16S NGS analysis. Moreover, 12 agro-morphological parameters were determined for grown wheat plants, and their results showed a high yield in the ‘Q’ soil compared to other soils; this could be attributed to the increased abundance of Proteobacteria and Actinobacteria, high enrichment in nutrients (N and K), or increased EC/nutrient availability. Ultimately, the potential use of a taxon-specific qPCR primer-panel as an alternative approach to NGS provides a cheaper, user-friendly setup with high accuracy.

Impact of gut microbiota composition on black cutworm, Agrotis ipsilon (hufnagel) metabolic indices and pesticide degradation

“…The bacterial isolates were identified based on their 16 S rRNA gene sequence. The genomic DNA template was used to amplify approximately 123 base pairs of the 16 S rRNA gene using the Bact1369F (5’CGGTGAATACGTTCYCGG3) and Prok1492R (5’GGWTACCTTGTTACGACTT3) primers [ 4 , 84 , 92 ]. PCR reactions were performed using amaR OnePCR Master Mix (GeneDireX, Taiwan, China) and 10 pmol of each primer.…”

Role of Plant Growth Promoting Rhizobacteria in Healthy and Sustainable Agriculture

“…Therefore, researchers explore new approaches and ecofriendly methods to control plant diseases (Saraf et al, 2014;Carmona-Hernandez et al, 2019;Khalil, et al, 2023). PGPR has an essential role in protection of crops against phytopathogens in addition to improvement of soil health conditions (Fernando et al, 2005, Abdelmoneim et al, 2023. Also, usage of PGPR help in understanding the goals of world agriculture production to feed the world growing populations (Sayyed et al, 2019) .…”