Diversity of denitrifying microflora and ability to reduce N2O in two soils

Abstract

 The ozone-depleting gas N₂O is an intermediate in denitrification, the biological reduction of NO₃ ^– to the gaseous products N₂O and N₂ gas. The molar ratio of N₂O produced (N₂O/N₂O+N₂) varies temporally and spatially, and in some soils N₂O may be the dominant end product of denitrification. The fraction of NO₃ ^–-N emitted as N₂O may be due at least in part to the abundance and activity of denitrifying bacteria which possess N₂O reductase. In this study, we enumerated NO₃ ^–-reducing and denitrifying bacteria, and compared and contrasted collections of denitrifying bacteria isolated from two agricultural soils, one (Auxonne, soil A) with N₂O as the dominant product of denitrification, the other (Châlons, soil C) with N₂ gas as the dominant product. Isolates were tested for the ability to reduce N₂O, and the presence of the N₂O reductase (nosZ)-like gene was evaluated by polymerase chain reaction (PCR) using specific primers coupled with DNA hybridization using a specific probe. The diversity and phylogenetic relationships of members of the collections were established by PCR/restriction fragment length polymorphism of 16s rDNA. The two soils had similar numbers of bacteria which used NO₃ ^– as a terminal electron acceptor anaerobically. However, the soil A had many more denitrifiers which reduced NO₃ ^– to gaseous products (N₂O or N₂) than did soil C. Collections of 258 and 281 bacteria able to grow anaerobically in the presence of NO₃ ^– were isolated from soil A and soil C, respectively. These two collections contained 66 and 12 denitrifying isolates, respectively, the others reducing NO₃ ^– only as far as NO₂ ^–. The presence of nosZ sequences was generally a poor predictor of N₂O reducing ability: there was agreement between the occurrence of nosZ sequences and the N₂O reducing ability for only 42% of the isolates; 35% of the isolates (found exclusively in soil A) without detectable nosZ sequences reduced N₂O whereas 21% of the isolates carrying nosZ sequences did not reduce this gas under our assay conditions. Twenty-eight different 16S rDNA restriction patterns (using two restriction endonucleases) were distinguished among the 78 denitrifying isolates. Two types of patterns appeared to be common to both soils. Twenty-three and three types of patterns were found exclusively among bacteria isolated from soils A and C, respectively. The specific composition of denitrifying communities appeared to be different between the two soils studied. This may partly explain the differences in the behaviour of the soils concerning N₂O reduction during denitrification.