title: Comparison of the abundance and community structure of ammonia oxidizing prokaryotes in rice rhizosphere under three different irrigation cultivation modes.
abstract: The abundance, diversity and community structure of ammonia oxidizing archaea (AOA) and bacteria (AOB) in rice rhizosphere soils under three different irrigation cultivated modes, named continuous irrigation mode (C), intermittent irrigation mode (I) and semi-arid mode (M), respectively, were investigated using amoA gene as a molecular biomarker. Clone libraries and quantitative polymerase chain reaction results indicated the highest number of archaeal amoA gene copy was detected in M cultivation mode, then in I and C, whereas, their order of amoA gene copy numbers were I > M > C for AOB, and those were obvious higher than in the bulk soil. The ratios of AOA/AOB were greater than 1 for all samples, suggested the predominance of AOA throughout the period of rice growth in the three different irrigation cultivation modes. Diversity index (SChao1 and Shannon H) have an obvious variation in three different irrigation cultivation modes. For AOA, SChao1 was highest in M and lowest in I mode, whereas, Shannon H was highest in M cultivation mode and lowest in C mode. For AOB, mode M exhibited the highest diversity index (SChao1 and Shannon H), while C showed the lowest highest diversity, suggested long-term water input (continuous mode) may decrease diversity of ammonia oxidizers, whereas mode M may be more appropriate for them. In addition, AOA sequences fall within Nitrososphaera, Nitrosopumilus and Nitrosotalea cluster with proportion of 89.38, 8.85 and 1.77 %, respectively. AOB gene sequences belonged to the Nitrosomonas and Nitrosospira genera with proportion of 90.97 and 9.03 %, respectively. In addition, the abundances, diversity and community structure had an obvious temporal variation in three developmental stages of rice, further suggested rice growth obviously affected the ammonia oxidizing prokaryotes in their rhizosphere soil.
authors.affiliation: Department of Environment Engineering, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China.
authors.forename: Jinping
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Environment Engineering, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China. xhzhou0214@163.com.
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Department of Environment Engineering, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.affiliation: Department of Environment Engineering, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Environment Engineering, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China.
authors.forename: Jinyu
authors.initials: J
authors.lastname: Chu
authors.affiliation: Department of Environment Engineering, School of the Environment and Safety Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, People's Republic of China.
authors.forename: Yimin
authors.initials: Y
authors.lastname: Li
mesh_terms: D057914:Agricultural Irrigation / Q000379:methods*; D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D044822:Biodiversity; D012275:Oryza / Q000254:growth & development / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny; D058441:Rhizosphere; D012988:Soil Microbiology; D014867:Water / Q000378:metabolism
chemical_list: D014867:Water; D000641:Ammonia
keywords: Ammonia oxidizing archaea; Ammonia oxidizing bacteria; Moisture; Phylogeny; Rice rhizosphere