Ammonium availability and temperature control contributions of ammonia oxidizing bacteria and archaea to nitrification in an agricultural soil

Ouyang, Yang; Norton, Jeanette M.; Stark, John

doi:10.1016/j.soilbio.2017.06.010

Cited by 159 publications

(97 citation statements)

References 56 publications

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“…We found that the application of lime increased the abundance of AOB and substantially enhanced nitrification activity. While this increase in nitrification activity may be a result of reduced ionization of NH 3 to NH 4 ϩ and a rise in the associated substrate availability under the increased-pH conditions and increased abundance of AOB, maximum rates of nitrification by AOB have been shown to be 20-fold higher than those by AOA (33).…”

Section: Discussionmentioning

confidence: 99%

“…However, genomic analysis suggested that AOA genes putatively encode pH homeostasis and high-affinity NH 3 acquisition systems (32) and thus could play a crucial role in nitrification in acidic soils where pH and NH 3 availability are particularly low (21). In contrast, AOB, which were also adapted to low soil pH (21), had a far lower substrate affinity than that of AOA (33), which suggests that AOA outcompeted AOB for substrates in the control soil. Our experiment showed that the long-term application of liming (NL) reduced AOA abundance, possibly because the increased soil pH reduced the competitive ability of AOA in soils (6,34).…”

Section: Discussionmentioning

confidence: 99%

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Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization

Lin

Luo

et al. 2018

Appl Environ Microbiol

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Long-term effects of inorganic and organic fertilization on nitrification activity (NA) and the abundances and community structures of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated in an acidic Ultisol. Seven treatments applied annually for 27 years comprised no fertilization (control), inorganic NPK fertilizer (N), inorganic NPK fertilizer plus lime (CaCO) (NL), inorganic NPK fertilizer plus peanut straw (NPS), inorganic NPK fertilizer plus rice straw (NRS), inorganic NPK fertilizer plus radish (NR), and inorganic NPK fertilizer plus pig manure (NPM). In nonfertilized soil, the abundance of AOA was 1 order of magnitude higher than that of AOB. Fertilization reduced the abundance of AOA but increased that of AOB, especially in the NL treatment. The AOA communities in the control and the N treatments were dominated by the and B1 clades but shifted to clade A in the NL and NPM treatments. cluster 8a was found to be the most dominant AOB in all treatments. NA was primarily regulated by soil properties, especially soil pH, and the interaction with AOB abundance explained up to 73% of the variance in NA. When NL soils with neutral pH were excluded from the analysis, AOB abundance, especially the relative abundance of cluster 8a, was positively associated with NA. In contrast, there was no association between AOA abundance and NA. Overall, our data suggest that cluster 8a of AOB played an important role in the nitrification process in acidic soil following long-term inorganic and organic fertilization. The nitrification process is an important step in the nitrogen (N) cycle, affecting N availability and N losses to the wider environment. Ammonia oxidation, which is the first and rate-limiting step of nitrification, was widely accepted to be mainly regulated by AOA in acidic soils. However, in this study, nitrification activity was correlated with the abundance of AOB rather than that of AOA in acidic Ultisols. cluster 8a, a phylotype of AOB which preferred warm temperatures, and low soil pH played a predominant role in the nitrification process in the test Ultisols. Our results also showed that long-term application of lime or pig manure rather than plant residues altered the community structure of AOA and AOB. Taken together, our findings contribute new knowledge to the understanding of the nitrification process and ammonia oxidizers in subtropical acidic Ultisol under long-term inorganic and organic fertilization.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization

Lin

Luo

et al. 2018

Appl Environ Microbiol

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“…However, the declined ammonia supply, which was a result of decreased GNM (Figure ) and increased microbial NH 4 + immobilization during the middle and late thaw stages (Figure S3), could induce inhibiting effects on gross nitrification. Specifically, the decline in ammonia supply could directly decrease soil nitrification (Kou et al, ) and also indirectly suppress gross nitrification by inhibiting the growth of AOA and AOB (Table ) since ammonia as a substrate is an important driving factor for these ammonia oxidizers (Ouyang et al, ). Consequently, the tradeoff between higher oxygen availability and lower ammonia supply could result in similar topsoil gross nitrification between the control and the middle and late thaw stages.…”

Section: Discussionmentioning

confidence: 99%

“…It has been reported that these ammonia oxidizers are generally sensitive to the variation in soil water availability and prefer to grow under aerobic conditions (Gleeson et al, 2010). Given that AOA and AOB mediate the first step of nitrification (Ouyang et al, 2017), increased abundances of these ammonia oxidizers could have a positive effect on nitrification (Mcleod et al, 2016;Merbt et al, 2016).…”

Section: Accelerated Topsoil Gross Nitrification During the Early Permentioning

confidence: 99%

Trajectory of Topsoil Nitrogen Transformations Along a Thermo‐Erosion Gully on the Tibetan Plateau

et al. 2019

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Permafrost thaw, especially thermokarst formation, that is, ground collapse due to thawing of ice‐rich permafrost, is expected to alter soil gross nitrogen (N) transformations, which can regulate plant productivity and ecosystem carbon cycle. However, it remains unclear how thermokarst formation modifies soil N processes in permafrost ecosystems. Here 15N pool dilution techniques were used to evaluate changes in topsoil gross N transformations during various thaw stages (early, middle, and late stages) along a thermo‐erosion gully on the Tibetan Plateau. Structural equation modeling was then conducted to explore the relative importance of biotic and abiotic factors in affecting soil gross N transformations. The results showed that topsoil gross N mineralization (GNM) decreased at the three stages, reflecting declined inorganic N production after permafrost collapse. In contrast, topsoil gross nitrification increased only during the early stage. Additionally, the ratio of microbial N immobilization to GNM was enhanced during the middle and late stages, indicating a stronger microbial N limitation after thermokarst formation. The structural equation modeling analysis revealed that soil moisture played an important role in modulating gross N transformations. For GNM, decreased soil moisture had inhibiting effects via regulating the microbial biomass, microbial community, and enzyme activities along the thaw sequence. For gross nitrification, declined soil moisture exerted facilitating effects directly by improving oxygen availability and indirectly by modulating the abundances of ammonia‐oxidizing archaea and bacteria during the early stage. Overall, these results demonstrated that thermokarst formation altered soil N processes, potentially triggering interactions between ecosystem N and carbon cycles after permafrost thaw.

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“…In addition, AOB abundance has been found to increase after the application of nitrogen fertilizers [15,16]. Numerous factors affect nitrification mechanisms and microbial communities associated with AOA and AOB in soil, such as habitat type, soil temperature, soil pH and the application of nitrogen fertilizers [17][18][19][20][21][22]. The effects of a wide range of factors on the nitrification processes in paddy soils have been discussed, such as soil types [23], availability of ammonium [15,16] and pH levels [24,25].…”

Section: Introductionmentioning

confidence: 99%

Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review

2017

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Ammonia oxidation is crucial in nitrogen removal and global nitrogen dynamics since it is the first step of the nitrification process. In this review, we focus on the distribution and community structure of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in East Asian paddy soils with variable soil properties. The available East Asian paddy soil data shows that the ammonium concentration and pH ranges from 0.4 to 370 mg/kg and 5.1 to 8.2, respectively. Our meta-analysis suggest that AOA specific gene sequences are generally more abundant than those of AOB in both acidic and alkaline paddy soils, where Nitrosophaera and Nitrosospira amoA clusters mainly dominate the microbial community, respectively. In addition, the contribution of ammonia oxidizers to the nitrification process has been demonstrated using DNA-SIP (DNA-based stable-isotope probing); the results of these studies indicate that pH is the most important factor in niche separation of AOA and AOB under a variety of edaphic conditions. Finally, we discuss a number of other environmental variables that affect the abundance, distribution, and activity of AOA and AOB in East Asian paddy soils.

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Ammonium availability and temperature control contributions of ammonia oxidizing bacteria and archaea to nitrification in an agricultural soil

Cited by 159 publications

References 56 publications

Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization

Nitrosospira Cluster 8a Plays a Predominant Role in the Nitrification Process of a Subtropical Ultisol under Long-Term Inorganic and Organic Fertilization

Trajectory of Topsoil Nitrogen Transformations Along a Thermo‐Erosion Gully on the Tibetan Plateau

Ammonia Oxidizing Archaea and Bacteria in East Asian Paddy Soils—A Mini Review

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