Feb 27, 2013

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil

Environmental Microbiology
Xiubin KeRalf Conrad

Abstract

The dynamics of populations and activities of ammonia-oxidizing and nitrite-oxidizing microorganisms were investigated in rice microcosms treated with two levels of nitrogen. Different soil compartments (surface, bulk, rhizospheric soil) and roots (young and old roots) were collected at three time points (the panicle initiation, heading and maturity periods) of the season. The population dynamics of bacterial (AOB) and archaeal (AOA) ammonia oxidizers was assayed by determining the abundance (using qPCR) and composition (using T-RFLP and cloning/sequencing) of their amoA genes (coding for a subunit of ammonia monooxygenase), that of nitrite oxidizers (NOB) by quantifying the nxrA gene (coding for a subunit of nitrite oxidase of Nitrobacter spp.) and the 16S rRNA gene of Nitrospira spp. The activity of the nitrifiers was determined by measuring the rates of potential ammonia oxidation and nitrite oxidation and by quantifying the copy numbers of amoA and nxrA transcripts. Potential nitrite oxidation activity was much higher than potential ammonia oxidation activity and was not directly affected by nitrogen amendment demonstrating the importance of ammonia oxidizers as pace makers for nitrite oxidizer populations. Marked differenc...Continue Reading

Mentioned in this Paper

Microorganism
Real-Time Polymerase Chain Reaction
Gene Dosage
Nitrosospira
Genus Nitrospira
Oxidase
Transcription Initiation
Oxidation Activity [MoA]
Ammonia monooxygenase
Archaea

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