Acidic soils (pH<5.5) are widely distributed in tropical and subtropical area of China using as grain and economic crops producing land. For a long time, ammonia-oxidizing bacteria (AOB) were thought to be the main drivers of soil nitrification processes. However, AOB could not be detected in some acidic soils, or the presence of AOB was not responsible for the observed active nitrification in the acid soils. Therefore, the underpinning mechanisms of nitrification in acidic soils remain poorly understood.
In a survey on soil nitrifier diversity, the team led by professor He Jizheng at Research Center for Eco-Environmental Sciences (RCEES), Chinese Academy of Sciences, firstly found that ammonia-oxidizing archaea (AOA) presented in acidic red soils with higher abundance than AOB, and that the abundance of AOA positively correlated with the potential nitrification rates (PNR), implying the potential important role of AOA in acidic soil nitrification. These findings were published in Environmental Microbiology in 2007 and were widely cited in the subsequent studies (> 150 times by SCI journal papers up to now). Recently, by using stable isotope probing (SIP) technique combining with the molecular microbial ecological methods, they further investigated the nitrification mechanism in acidic soils.
In this work, they incubated the typical acidic soils with 13C-CO2 in laboratory microcosm and separated 13C-labelled DNA from 12C DNA by the density gradient centrifugation, assuming that ammonia oxidizers are chemolithoautotrophic and can fix CO2 as the sole carbon source. Further DNA analysis showed that 13C-CO2 was only incorporated into the archaeal amoA gene (the key functional gene encoding ammonia monooxygenase subunit A), not into the bacterial amoA gene. Significantly positive correlations between nitrate concentration and amoA gene of AOA, but not AOB, was also observed during the incubation. Two AOA groups, affiliating within the Thaumarchaeota phylum, obviously increased during the active nitrification. These results clearly demonstrated that AOA over AOB dominated the nitrification processes in the tested acidic soils, which for the first time directly linked the ammonia oxidation activity in acidic soil ecosystems to AOA.
The results have been published in The ISME Journal in May, 2012 (Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils. The ISME J, 6(5): 1032-1045). As a newly recognized archaeal phylum, the recent research progress on Thaumarchaeota was reviewed by the group in Acta Microbiologica Sinica (Zhang LM and He JZ, 2012, 52: 411-421).
The link of the abstract: http://www.nature.com/ismej/journal/v6/n5/abs/ismej2011168a.html?WT.ec_id=ISMEJ-201205.
