title: Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from South China.
abstract: While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg-1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils.
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Yuan
authors: Y
authors: Liu
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Yongzhuo
authors: Y
authors: Liu
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Yuanjun
authors: Y
authors: Ding
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Jinwei
authors: J
authors: Zheng
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Tong
authors: T
authors: Zhou
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China; Center of Ecosystem Carbon Sink and Environment Remediation, Zhejiang Agricultural and Forestry University, Linan, Hangzhou, China.
authors: Genxing
authors: G
authors: Pan
authors: Department of Environment Sciences, University of California Riverside, Riverside, California, United States of America.
authors: David
authors: D
authors: Crowley
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Lianqing
authors: L
authors: Li
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Jufeng
authors: J
authors: Zheng
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Xuhui
authors: X
authors: Zhang
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Xinyan
authors: X
authors: Yu
authors: Institute of Resource, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing, China.
authors: Jiafang
authors: J
authors: Wang
mesh_terms: D000641:Ammonia / Q000378:metabolism; D001105:Archaea / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D002681:China; D058440:Denitrification / Q000235:genetics*; D004787:Environmental Pollution; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D019216:Metals, Heavy / Q000378:metabolism; D059013:Microbial Consortia / Q000235:genetics; D008906:Mining; D008969:Molecular Sequence Data; D012275:Oryza / Q000254:growth & development; D010084:Oxidation-Reduction; D010802:Phylogeny; D012988:Soil Microbiology
chemical_list: D019216:Metals, Heavy; D000641:Ammonia