Abstract
Abstract. The function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) depends on the major energy-generating compounds (i.e., ammonia and oxygen). The diversification of AOA and AOB communities along ecological gradients of substrate availability in a complex environment have been much debated but rarely tested. In this study, two ecosystems of maize and rice crops under different fertilization regimes were selected to investigate the community diversification of soil AOA and AOB upon conversion of an upland field to a paddy field and long-term field fertilization in an acid soil. Real-time quantitative polymerase chain reaction of ammonia monooxygenase (amoA) genes demonstrated that the abundance of AOA was significantly stimulated after conversion of upland to paddy soils for more than 100 yr, whereas a slight decline in AOB numbers was observed. Denaturing gradient gel electrophoresis fingerprints of amoA genes further revealed remarkable changes in the community compositions of AOA after conversion of aerobic upland to flooded paddy field. Sequencing analysis revealed that upland soil was dominated by AOA within the soil group 1.1b lineage, whereas the marine group 1.1a-associated lineage predominated in AOA communities in paddy soils. Irrespective of whether the soil was upland or paddy soil, long-term field fertilization led to increased abundance of amoA genes in AOA and AOB compared with control treatments (no fertilization), whereas archaeal amoA gene abundances outnumbered their bacterial counterparts in all samples. Phylogenetic analyses of amoA genes showed that Nitrosospira cluster-3-like AOB dominated bacterial ammonia oxidizers in both paddy and upland soils, regardless of fertilization treatment. The results of this study suggest that the marine group 1.1a-associated AOA will be better adapted to the flooded paddy field than AOA ecotypes of the soil group 1.1b lineage, and indicate that long-term flooding is the dominant selective force driving the community diversification of AOA populations in the acid soil tested.
Highlights
Ammonia-oxidizing arOchcaeea a(AnOAS)canied nbaccteeria (AOB) play central roles in the biogeochemical cycle of nitrogen
Similar results were obtained for paddy soils, long-term field fertilization affected soil properties to a lesser extent in paddy soils compared with upland soils
Our results indicated that AOA within the marine 1.1a-associated lineage might be better adapted to flooded paddy soils than soil group 1.1b AOA, and conversion of an upland field to a flooded paddy field plays a key role in the divergence of AOA communities in acid soil
Summary
Methods and DataSystemsReceived: 13 January 2013 – Published in Biogeosciences Discuss.: 31 January 2013Revised: 14 July 2013 – Accepted: 22 July 2013 – Published: 30 August 2013 AbstractThe function of ammonia-oxidizing archaeaGeoscientific treatment. Sciences versification of soil AOA and AOB upon conversion of an upland field to a paddy field and long-term field fertilization 1 Introduction. Phylogenetic analyses of amoA genes showed that Nitrosospira cluster-3-like AOB dominated bacterial ammonia oxidizers in both paddy and upland soils, regardless of fertilization. The region has a typical subtropical monsoon climate with a mean annual precipitation of 1727 mm, mean annual evaporation of 1318 mm and a mean annual temperature of 18.1 ◦C with approximately 262 days without frost per year Both paddy and upland soils originated from quaternary red clay with dominant kaolinitic minerals and were classified as a Haplic Stangnic Anthrosol according to USDA soil taxonomy. The long-term field fertilization experiment of upland soil was initiated in 1986 approximately 150 m from the paddy field experiment site. The crop rotation system for upland soils includes early maize (Zea mays L.) from April to July, late maize from July to October and winter fallow from
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