Autotrophic growth of nitrifying community in an agricultural soil

• Published in: The ISME Journal Vol. 5; no. 7; pp. 1226 - 1236
• Main Authors: Xia, Weiwei, Zhang, Caixia, Zeng, Xiaowei, Feng, Youzhi, Weng, Jiahua, Lin, Xiangui, Zhu, Jianguo, Xiong, Zhengqin, Xu, Jian, Cai, Zucong, Jia, Zhongjun
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.07.2011; Oxford University Press; Nature Publishing Group
• Subjects: 631/326/171/1818; 631/326/2565/855; 631/443/319; Agricultural land; Agriculture; Ammonia; Ammonia - metabolism; Ammonium; Archaea - classification; Archaea - genetics; Archaea - growth & development; Autotrophic Processes; Bacteria - classification; Bacteria - genetics; Bacteria - growth & development; Biomedical and Life Sciences; Carbon dioxide; Deoxyribonucleic acid; DNA; Ecology; Evolutionary Biology; Gene Library; Genes, Archaeal; Genes, Bacterial; Genes, rRNA; High-Throughput Nucleotide Sequencing; Hot springs; Incubation; Life Sciences; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microcosms; Nitrification; Nitrites - metabolism; Nitrogen cycle; Original; original-article; Oxidation; Phylogeny; Sequence Analysis, DNA; Soil - analysis; Soil environment; Soil Microbiology; Soil testing; Soils; Stable isotopes; ammonia-oxidizing bacteria; stable isotope probing; pyrosequencing; nitrite-oxidizing bacteria; agricultural soil; ammonia-oxidizing archaea
• ISSN: 1751-7362; 1751-7370; 1751-7370
• DOI: 10.1038/ismej.2011.5

The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by 13 CO 2 after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the 13 C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira -like NOB in the 13 C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter -like NOB. Furthermore, the acetylene inhibition technique showed that 13 CO 2 assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested.