Insights into the abundance, expression and diversity of key denitrification genes in an ecologically managed greenhouse agricultural soil

• Published in: Applied biological chemistry Vol. 67; no. 1; pp. 43 - 10
• Main Authors: Hernández Maqueda, R., Ballesteros, I., Meca, D., Linacero, R., del Moral, F.
• Format: Journal Article
• Language: English
• Published: Singapore Springer Nature Singapore 01.12.2024; Springer Nature B.V; SpringerOpen; 한국응용생명화학회
• Subjects: Abundance; Agricultural land; Applied Microbiology; Biological Techniques; Bioorganic Chemistry; Chemistry; Chemistry and Materials Science; Cloning; Crop residues; Denitrification; Denitrifying genes; Deoxyribonucleic acid; DNA; Farm buildings; Gene expression; Genes; Greenhouse gases; Greenhouses; mRNA; nirK; nirS; Nitrification; Nitrous oxide; nosZ; Phylogeny; Polymerase chain reaction; Sequence analysis; Soil bacteria; Soil management; Soil microorganisms; Soil types; Soils; 농학; Denitrifying genes; Nitrous oxide
• ISSN: 2468-0842; 2468-0834; 2468-0842
• DOI: 10.1186/s13765-024-00901-x

Understanding the bacteria associated with nitrification and denitrification is crucial for comprehending the processes that lead to nitrous oxide emissions in agricultural greenhouse soils. Therefore, it is important to determine their abundance and expression to gain insight into these processes. The aim of this study was to explore the bacterial communities associated with denitrification in a greenhouse agricultural soil amended with crop residues and manure for six years. For this purpose, we proceeded to detect and quantify the genes nirK and nirS and the gene nosZ through clone library construction, sequencing, phylogenetic analysis, and quantitative polymerase chain reaction (qPCR). Sequence analysis based on the clone library revealed that many of the nirS or nirK genes detected were not closely related to known denitrifier bacteria, but some of the nosZ sequences were related to the genera such as Pseudomonas , Halomonas , and Marinobacter . Furthermore, the qPCR revealed a high abundance of DNA copies in nirK , 6.08 × 10 9 ± 1.16 × 10 9 , while nirS and nosZ showed lower values, 9.05 × 10 6 ± 1.65 × 10 6 and 8.71 × 10 6 ± 1.44 × 10 6 , respectively. However, the highest expression rate was observed for nirS (mRNA/DNA ratio = 3.10 × 10 − 3 ), while nirK and nosZ showed 10-fold lower expression rates (4.4 × 10 − 4 and 3.5 × 10 − 4 , respectively). The results of this work provide a preliminary overview of the diversity, abundance and expression of key genes associated with the denitrification process in this type of soil and are a starting point for further studies to understand how this type of soil management can influence the denitrification process.