Effect of elevated atmospheric CO2 concentration on ammonia oxidizing bacteria communities inhabiting in rice roots

Recent research suggests that rice root characteristics, particularly growth, are altered by elevated atmospheric CO2. Thus, microbial communities existing in or on rice roots could be greatly influenced by atmospheric CO2 concentration. We investigated the effect of elevated atmospheric CO2 on ammonia oxidizing bacteria (AOB) communities associated with rice roots using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing methods. Rice roots were collected from rice fields in a free-air CO2 enrichment experiment at Shizukuishi, Japan. Differences in DGGE banding patterns among elevated atmospheric CO2 and ambient treatments, young and old roots and rice growth stages were evident. Principal component analysis indicated that AOB communities in rice roots were influenced mainly by rice growth stage, although there was a tendency for communities from elevated CO2 conditions to be different from communities under ambient conditions. Both Nitrosospira-like and Nitosomonas-like AOB sequences were detected in the rice roots tested. Close relatives of Nitrosospira sp. NpAV strain were likely to be the most dominant AOB inhabiting rice roots in the experimental paddy field. Although the DGGE band patterns showed a possible difference between ambient and elevated CO2, under both CO2 levels the bands that were sequenced were predominately Nitrosospira spp. with AmoA clusters 1 and 2.