Biochemical pathways used by microorganisms to produce nitrous oxide emissions from soils fumigated with dimethyl disulfide or allyl isothiocyanate

Abstract

Abstract Despite using fumigants for many decades to control soil-borne pathogens and plant-parasitic nematodes, the influence of soil fumigation on microorganisms involved in the nitrogen-transforming process remains little understood. We used real-time PCR (quantitative polymerase chain reaction) and 16S rRNA gene amplicon sequencing techniques to determine nitrous oxide (N2O) emissions from bacterial microorganisms associated with nitrogen (N) transfer when soils were fumigated with dimethyl disulfide (DMDS) or allyl isothiocyanate (AITC). Our results showed that fumigation with DMDS or AITC increased N2O emissions 6.5–7.3 and 11.2–20.7 times, respectively. The abundance of 16S rRNA and N cycling functional genes initially decreased, but recovered to the unfumigated levels after fumigation. N2O emissions were significantly correlated to the presence of NH4+, NO3−, dissolved amino acids (DAA) and microbial biomass nitrogen (MBN). N2O emissions were not correlated with the abundance of N-transforming functional genes. Metatranscriptomes and dual-label 15N 18O isotope anaylsis revealed DMDS fumigation significantly increased the expression of gene families involved in the N-transforming process, but depressed ammonia oxidation which caused a shift in the N2O pathway from nitrification to denitrification. However, AITC fumigation suppressed most genes involved in the N cycle, but increased the expression of genes that transformed NO2− to NO and further organic decomposition, so that overall there was a shift in the N2O pathway from nitrification to nitrifier denitrification. The information obtained in this study will provide further insights into the N cycling pathways in fumigated soils and into the potential responses of different N-cycling groups after fumigation.