Autotrophic growth of nitrifying community in an agricultural soil

Abstract

The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by 13 CO 2 after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the 13 C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the 13 C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that 13 CO 2 assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested. The ISME Journal (2011) 5, 1226-1236; doi:10.1038/ismej.2011.5; published online 17 February 2011Subject Category: microbial ecology and functional diversity of natural habitats

Effects of intercropping and Rhizobial inoculation on the ammonia-oxidizing microorganisms in rhizospheres of maize and faba bean plants

“…The archaea have previously been widely found in soils (Sims et al, 2012;Taylor et al, 2012), and they can be distinguished from bacteria by their adaptation to chronic energy stress (Valentine, 2007), but their ecological roles are still not well known. The greater abundance of AOA (24.5 and 2.3 times more) than AOB in the rhizospheres of maize and faba bean is consistent with some previous reports in agricultural soils (Leininger et al, 2006;Sims et al, 2012), but differed from the result of Xia et al (2011) who reported that AOB were dominated for the nitrification process in an agricultural soil. Two factors, soil pH value and NH 4 + content, have been evidenced to be the determinants for the ratio of AOA:AOB.…”

Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils

“…acidic conditions, which could block the direct delivery of fresh ammonia substrates to ammonia oxidizers. A previous study found that autotrophic ammonia oxidation was dominated by AOA in a pH 7.5 grassland soil without the external nitrogen supply , and contrasting findings demonstrated that AOB rather than AOA controlled the nitrification in two agricultural soils with weekly nitrogen fertilization at pH 7.0 (Jia and Conrad, 2009) and 8.0 (Xia et al, 2011), respectively. These three DNA-SIP incubations have a similar soil pH range, but differ in the availability of ammonia substrate.…”

“…Because of the development of new technologies like DNA-stable isotope probing (SIP), we could now be able to gain a deep insight into the autotrophic nitrification activity in complex soil environments. 13 CO 2 -DNA-SIP has shown its powerful potential to directly link CO 2 -incorporating ammonia oxidizers with nitrification activity in several neutral or alkaline soils (Jia and Conrad, 2009;Zhang et al, 2010;Pratscher et al, 2011;Xia et al, 2011) and provided evidence for autotrophic growth of N. devanaterra in acidic soil, whereas to the best of our knowledge, no study has been able to clearly identify the dominating ammonia oxidizers in the autotrophic nitrification of acidic soils.…”

Dynamics of ammonia-oxidizing archaea and bacteria populations and contributions to soil nitrification potentials

“…A case can be made that the relative contributions of AOA and AOB to soil nitrification might shift in different phases of crop rotation and during different seasons of the year. Although recent studies have evaluated AOA and AOB population sizes, composition and/or their relative growth responses in soils recovered from agricultural cropping systems, the soils were often taken from complex crop rotations in multi-year cycles, and sampled in either spring, fall or unspecified times (Tourna et al, 2008;Hallin et al, 2009;Wessen et al, 2010Wessen et al, , 2011Xia et al, 2011). Clearly, the extent to which phase of the crop rotation or time of soil sampling might have influenced the results cannot be determined.…”