title: Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.
abstract: Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.
authors.affiliation: College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: He
authors.initials: H
authors.lastname: Song
authors.affiliation: College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Che
authors.affiliation: College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
authors.forename: Wenchao
authors.initials: W
authors.lastname: Cao
authors.affiliation: College of Agronomy, Anhui Agricultural University, Hefei, 230036, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Huang
authors.affiliation: College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
authors.forename: Jingguo
authors.initials: J
authors.lastname: Wang
authors.affiliation: College of Agronomy, Anhui Agricultural University, Hefei, 230036, China. songhesonghe@foxmail.com.
authors.forename: Zhaorong
authors.initials: Z
authors.lastname: Dong
mesh_terms: D000641:Ammonia / Q000737:chemistry; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D020562:Betaproteobacteria / Q000235:genetics; D005308:Fertilizers; D006863:Hydrogen-Ion Concentration; D059013:Microbial Consortia / Q000187:drug effects*; D058465:Nitrification; D009584:Nitrogen / Q000737:chemistry / Q000494:pharmacology*; D010084:Oxidation-Reduction; D010802:Phylogeny; D060888:Real-Time Polymerase Chain Reaction; D012987:Soil / Q000737:chemistry*; D012988:Soil Microbiology
chemical_list: D005308:Fertilizers; D012987:Soil; D000641:Ammonia; D009584:Nitrogen
keywords: Community shift; Nitrification potential; Pyrosequencing techniques; Soil acidification; amoA gene