title: High Oxygen Concentration Increases the Abundance and Activity of Bacterial Rather than Archaeal Nitrifiers in Rice Field Soil.
abstract: Oxygen is considered as a limiting factor for nitrification in rice paddy soil. However, little is known about how the nitrifying microbial community responds to different oxygen concentrations at community and transcript level. In this study, soil and roots were harvested from 50-day-old rice microcosms and were incubated for up to 45 days under two oxygen concentrations: 2 % O(2) and 20 % O(2) (ambient air). Nitrification rates were measured from the accumulation of nitrite plus nitrate. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was determined from the abundance (using quantitative PCR (qPCR)) and composition (using terminal restriction fragment length polymorphism and cloning/sequencing) of their amoA genes, that of nitrite oxidizers (NOB) by quantifying the nxrA gene of Nitrobacter spp. and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by quantifying the copy numbers of amoA and nxrA transcripts (using RT-qPCR). Different oxygen concentrations did not affect the community compositions of AOB, AOA, and NOB, which however were different between surface soil, bottom soil, and rice roots. However, nitrification rates were higher under ambient air than 2 % O(2), and abundance and transcript activities of AOB, but not of AOA, were also higher. Abundance and transcript copy numbers of Nitrobacter were also higher at ambient air. These results indicate that AOB and NOB, but not AOA, were sensitive to oxygen availability.
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.|Department Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse10, 35043, Marburg, Germany.
authors.forename: Xiubin
authors.initials: X
authors.lastname: Ke
authors.affiliation: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Lu
authors.affiliation: Department Biogeochemistry, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse10, 35043, Marburg, Germany. conrad@mpi-marburg.mpg.de.
authors.forename: Ralf
authors.initials: R
authors.lastname: Conrad
mesh_terms: D000641:Ammonia / Q000378:metabolism; D001105:Archaea / Q000254:growth & development / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D044822:Biodiversity; D006863:Hydrogen-Ion Concentration; D058465:Nitrification; D009573:Nitrites / Q000378:metabolism; D009576:Nitrobacter / Q000254:growth & development / Q000378:metabolism*; D012275:Oryza / Q000382:microbiology*; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics / Q000378:metabolism; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D001426:Bacterial Proteins; D009573:Nitrites; D012336:RNA, Ribosomal, 16S; D012987:Soil; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase; D010100:Oxygen
keywords: Ammonia monooxygenase; Ammonia-oxidizing bacteria; Ammonium-oxidizing archaea; Nitrification rate; Nitrite-oxidizing bacteria; Nitrobacter; Nitrospira; T-RFLP; Transcription; qPCR