Functional diversity and abundance of nitrogen cycle-related genes in paddy soil

Abstract

The nitrogen cycle and the associated microbes play an important role in natural ecosystems, including terrestrial habitats; they also have a major effect on climate change. The aim of this study was to explore microbial communities in rice paddy soil by detecting and quantifying some key functional genes involved in the nitrogen cycle using molecular techniques such as conventional polymerase chain reaction (PCR), clone library construction, sequencing, phylogenetic analysis, and real-time PCR. The genes analyzed were as follows: nitrogenase reductase gene (nifH), hydrazine synthase gene (hzsA), nitrous oxide reductase gene (nosZ), copper-containing (nirK) and cytochrome cd1-containing (nirS) nitrite reductase genes, nitrite oxidoreductase gene (nxrB), and ammonium monooxygenase gene (amoA). The sequence assessment using the clone library targeting these genes revealed high diversity and dominance of bacterial communities. Furthermore, real-time PCR using SYBR green dye and some primers specific for each gene revealed the high abundance of nxrB (4.1 × 10 9 ± 0.4 × 10 9 copies g −1 soil) and low abundance of hzsA (4.0 × 10 5 ± 1.1 × 10 5 copies g −1 soil). The findings of our study will be useful to explore microbial communities in terrestrial habitats, such as agricultural paddy fields. Publisher's NoteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Free and Immobilized Microbial Culture–Mediated Crude Oil Degradation and Microbial Diversity Changes Through Taxonomic and Functional Markers in a Sandy Loam Soil

“…The regulation of nitrogen cycling in the contaminated soil is vital to keep the soil microbial communities active and improve their potential to use the contaminant(s) as the sources of energy. Therefore, the status of ammonia oxygenase enzyme (encoded by amoA), nitrogenase enzyme (encoded by nifH, nifD, and nifK), nitrogen oxide reductase (nirK, nirS, and nosZ), and hydrazine synthase (hzsA mediated by annamox) can be the significant indices to determine the soil condition (Rubio and Ludden, 2002;Khanal and Lee, 2020). The present study indicated that nitrogen FIGURE 6 | PCA biplot depicting the taxonomic and functional gene markers of diverse microbial groups and treatments in crude oil fortified sandy loam soil [T1-soil; T2-soil + crude oil (1%); T3-soil + crude oil (1%) + bacterial consortia (Pseudomonas sp.…”

Phylogenetic Characterization of Nitrifying Bacteria Isolated from East Kolkata Wetland

“…The present study identifies a few nitrifying bacteria in EKW using molecular and computational techniques. A similar experiment was conducted by Khanal and Lee (2020), and established that these attempts provide better potential for analysis and assessment of AOB and NOB. In our study, we found nitrifying bacteria in EKW by analysing the phylogenetic relationship of 16S rRNAgene clusters.…”

“…amoA is the most relevant gene of AOB, thus they are widely used in community analysis research of water bodies and soil (He et al 2018;Malinowski et al 2020). nxrA gene is present in NOB and codes for the alpha subunit of nitrite oxidoreductase (Rani et al 2016) and helps in the oxidation of nitrite to nitrate (Khanal and Lee 2020). nxrA gene is widely used for the identification of NOB from different environmental samples (Ouyang and Norton 2020).…”

“…Similarly, this 16S rRNA sequence is used as a marker to explore the phylogenetic orientation of nitrifying bacterial community in water and soil samples. 16S rRNA genes analysis is a reliable tool for bacterialidentification (Khanal and Lee 2020). Capabilities of the 16S rRNA gene to establish the intragenomic diversity among bacteria were explored in this present study to establish the phylogenetic orientation.…”

Azohydromonas caseinilytica sp. nov., a Nitrogen-Fixing Bacterium Isolated From Forest Soil by Using Optimized Culture Method

“…Biological nitrogen fixation (BNF) is a key step in the nitrogen cycle as it transforms atmospheric nitrogen into ammonium (Pereira e Silva et al, 2013). The nitrogen cycle and the related microorganisms play crucial roles in the ecosystem, affecting both the agricultural field and climate sectors (Khanal and Lee, 2020). Strain G-1-1-14 T showed a direct association with the nitrogen cycle as it reported the ability to fix atmospheric nitrogen.…”