Phylogenetic and Functional Diversity of Denitrifying Bacteria Isolated from Various Rice Paddy and Rice-Soybean Rotation Fields

Abstract

Denitrifiers can produce and consume nitrous oxide (N2O). While little N2O is emitted from rice paddy soil, the same soil produces N 2 O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N 2 in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N 2 -producing denitrifiers.

Nitrogen Cycling in Rice Paddy Environments: Past Achievements and Future Challenges

“…These elongated cells were individually captured using a micromanipulator, and transferred to low-nutrient medium (9,43). Similar to the results obtained by culture-independent analyses, denitrifying bacteria belonging to various genera such as Bradyrhizobium, Dechloromonas, Herbaspirillum, and Pseudogulbenkiania were isolated from rice paddy soils (43,116). In addition, analysis of their nirK and nirS sequences revealed the presence of Bradyrhizobium denitrifiers carrying previously uncharacterized nirS sequences that have been detected only by culture-independent studies (43, 147, 148; Fig.…”

“…However, microbes responsive to denitrification-inducing conditions may vary by soil. For example, bacteria related to the genus Bradyrhizobium and Pseudogulbenkiania were the most frequently detected denitrifiers in rice paddy soils collected from different locations in Japan (47,116).…”

Identification and isolation of active N2O reducers in rice paddy soil

“…After incubation at 30 1C for 1 week, the amounts of 15 N-labeled N 2 and N 2 O were measured by GC/MS as described above. Denitrification activities of the strains were also measured in duplicate (two vials for each strain) by the acetylene block method (Tiedje, 1994) described previously Tago et al, 2011).…”

“…By analyzing the isolated strains, we were able to directly link the 16S rRNA gene and functional gene phylogenies. In addition, various cell properties, such as denitrification and N 2 O reduction rates, could also be measured (Tago et al, 2011).…”

Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002

“…strain NH8B, whose complete genomic sequence is available (8). The latter nitrate-reducing strain was isolated from agricultural paddy rice and soybean fields in Japan (12). It is anticipated that comparative genomics of P. ferrooxidans strain 2002 with other nitrate-dependent, Fe(II)-oxidizing bacteria will aid in the elucidation of the genetics underlying this globally important metabolism.…”