Analysis of the denitrification pathway and greenhouse gases emissions inBradyrhizobiumsp. strains used as biofertilizers in South America

Abstract

Aims: Greenhouse gases are considered as potential atmospheric pollutants, with agriculture being one of the main emission sources. The practice of inoculating soybean seeds with Bradyrhizobium sp. might contribute to nitrous oxide (N 2 O) emissions. We analysed this capacity in five of the most used strains of Bradyrhizobium sp. in South America. Methods and Results: We analysed the denitrification pathway and N 2 O production by Bradyrhizobium japonicum E109 and CPAC15, Bradyrhizobium diazoefficiens CPAC7 and B. elkanii SEMIA 587 and SEMIA 5019, both in freeliving conditions and in symbiosis with soybean. The in silico analysis indicated the absence of nosZ genes in B. japonicum and the presence of all denitrification genes in B. diazoefficiens strains, as well as the absence of nirK, norC and nosZ genes in B. elkanii. The in planta analysis confirmed N 2 O production under saprophytic conditions or symbiosis with soybean root nodules. In the case of symbiosis, up to 26.1 and 18.4 times higher in plants inoculated with SEMIA5019 and E109, respectively, than in those inoculated with USDA110. Conclusions: The strains E109, SEMIA 5019, CPAC15 and SEMIA 587 showed the highest N 2 O production both as free-living cells and in symbiotic conditions in comparison with USDA110 and CPAC7, which do have the nosZ gene. Although norC and nosZ could not be identified in silico or in vitro in SEMIA 587 and SEMIA 5019, these strains showed the capacity to produce N 2 O in our experimental conditions. Significance and Impact of the Study: This is the first report to analyse and confirm the incomplete denitrification capacity and N 2 O production in four of the five most used strains of Bradyrhizobium sp. for soybean inoculation in South America. À reductase enzymes encoded by the narG/napA genes. Nitrite reductase enzymes encoded by the nirS/nirK genes then reduce NO 2 À to nitric oxide (NO) and NO reductase encoded by the norB/norC genes reduce NO to nitrous oxide (N 2 O). Finally, N 2 O is reduced by N 2 O reductase, which is encoded by the nosZ gene. This leads to the formation of molecular nitrogen (N 2 ) as an end product (Bueno et al. 2012). However, not all denitrifying organisms have the genetic capacity for NO and N 2 O

New Insights into the Use of Rhizobia to Mitigate Soil N2O Emissions

“…On the contrary, inoculants based on nosZ − B. japonicum such as USDA138 would not be able to do so. This fact was also reported for soybean inoculation in South America [11,32], where the inoculant strains used are nosZ − and are unable to reduce N 2 O. Nevertheless, in situations with natural nodulating populations, more investigations are required on the competitiveness of selected strains in order to obtain a successful inoculation (i.e., the inoculant strain occupying a significant proportion of nodules formed on the roots).…”

Rhizobial Exopolysaccharides and Type VI Secretion Systems: A Promising Way to Improve Nitrogen Acquisition by Legumes

“…Bradyrhizobium inoculants are alternatives to reduce water pollution and nitrous oxide (N 2 O) emission (Akiyama et al, 2016). However, Obando et al (2019) showed the first report that pointed out the incomplete denitrification pathway in five of the most used strains for soybean. Göttfert et al (2001) described symbiosis-specific genes in a 410-kilobase DNA region of the B. diazoefficiens USDA110 chromosome and in 2002, the complete genomic sequence was described (Kaneko et al, 2002).…”

Sixteen Genome Sequences of Denitrifying Bacteria Assembled from Enriched Cultures of Anaerobic Pig Manure Digestate

“…The greenhouse gas N 2 O is produced during nitrification and denitrification ( 1 – 4 ). The N 2 O reductase encoded by the nosZ gene is the only enzyme that can reduce N 2 O to the nongreenhouse gas N 2 ( 5 – 8 ). In this study, bioinformatic tools were used for genome assembly and annotation of nosZ gene-containing bacterial genomes recovered from the metagenomic data for samples enriched with N 2 O.…”