The history of aerobic ammonia oxidizers: from the first discoveries to today

Monteiro, Maria; Séneca, Joana; Magalhães, Catarina

doi:10.1007/s12275-014-4114-0

Cited by 65 publications

(37 citation statements)

References 124 publications

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“…2, 3). The reason for this delay in nitrification may be due to the presence of a small nitrifying community in a soil with low natural pH (3.6 in the A horizon) and low NH 4 + concentrations, although the importance of these factors in understanding bacterial vs. archaeal contributions to nitrification in acidic soils is an area of current research (Prosser and Nicol, 2012; Monteiro et al, 2014). Nevertheless, the hydrolysis of urea to NH 4 + results in the transformation of an N source that is neutral and leachable to an N source that is positively charged and therefore less easily moved through the soil.…”

Section: Resultsmentioning

confidence: 99%

Urea Hydrolysis Rate in Soil Toposequences as Influenced by pH, Carbon, Nitrogen, and Soluble Metals

2016

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A simultaneous increase in the use of urea fertilizer and the incidence of harmful algal blooms worldwide has generated interest in potential loss pathways of urea from agricultural areas. The objective of this research was to study the rate of urea hydrolysis in soil profile toposequences sampled from the Coastal Plain (CP) and Piedmont (PM) regions of Maryland to understand native urea hydrolysis rates (UHRs) as well as the controls governing urea hydrolysis both across a landscape and with depth in the soil profile. A pH-adjustment experiment was conducted to explore the relationship between pH and urea hydrolysis because of the importance of pH to both agronomic productivity and microbial communities. Soils were sampled from both A and B horizons along transects containing an agricultural field (AG), a grassed field border (GB), and a perennially vegetated zone adjacent to surface water. On average, the A-horizon UHRs were eight times greater than corresponding B-horizon rates, and within the CP, the riparian zone (RZ) soils hydrolyzed urea faster than the agricultural soils. The pH adjustment of these soils indicated the importance of organic-matter-related factors (C, N, extractable metals) in determining UHR. These results suggest that organic-matter-rich RZ soils may be valuable in mitigating losses of urea from neighboring fields. Additional field-scale urea hydrolysis studies would be valuable to corroborate the mechanisms described herein and to explore the conditions affecting the fate and transport of urea in agroecosystems.

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Section: Resultsmentioning

confidence: 99%

Urea Hydrolysis Rate in Soil Toposequences as Influenced by pH, Carbon, Nitrogen, and Soluble Metals

2016

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“…Recent studies indicated that environmental drivers like substrate (i.e., NH 4 + ) concentration, pH, oxygen availability, salinity, among others, might be responsible for differentiating AOA and AOB abundance and distribution (Martens-Habbena and Stahl, 2011; Hatzenpichler, 2012; He et al, 2012; Prosser and Nicol, 2012; Zhalnina et al, 2012; Zhang et al, 2012). Despite previous attempts to evaluate drivers of natural AOA and AOB population dynamics, there remain large gaps in our understanding of factors that control AOA vs. AOB prominence in numerous ecosystems (Hatzenpichler, 2012; Prosser and Nicol, 2012; Monteiro et al, 2014). …”

Section: Introductionmentioning

confidence: 99%

The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

et al. 2014

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The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.

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“…Several types of microbial ammonia oxidation processes with different biochemical mechanisms are known to occur: the first is an aerobic oxidation of ammonia by chemolithotrophic ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and the second is an anaerobic process by ANAMMOX bacteria. The biochemical mechanisms of ammonia oxidation in the microorganisms have already been elucidated, and their ecological characteristics are also under the active investigation1234.…”

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confidence: 99%

Pyruvic oxime dioxygenase from heterotrophic nitrifier Alcaligenes faecalis is a nonheme Fe(II)-dependent enzyme homologous to class II aldolase

Tsujino

Uematsu

Dohra

et al. 2017

Sci Rep

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Pyruvic oxime dioxygenase (POD), a key enzyme in heterotrophic nitrification, was purified from Alcaligenes faecalis, and the molecular and catalytic characteristics were reexamined. POD was purified as the homotetramer of the subunit whose molecular weight was 30,000. The deduced amino acid sequence of POD was homologous with a class II aldolase that has been regarded as the Zn(II)-dependent enzyme catalyzing aldol reactions. The recombinant protein showed weak POD activity, and was activated by reconstitution with Fe(II). Affinity and catalytic constants were estimated at 470 μM and 4.69 sec−1, respectively. The POD was inactivated by EDTA to remove bound divalent metal cations. A reconstitution experiment demonstrated that Fe(II), not Zn(II), is essential for POD activity and that Mn(II) could partially fulfill the function of Fe(II). A mutant POD with replacement of His183, corresponding to one of three Zn(II)-binding ligands in the class II aldolase, by Asn was purified as a homotetrameric protein but showed no catalytic activities. Those results suggest that the POD is homologous to class II aldolase having non-heme Fe(II) as a catalytic center instead of Zn(II). A possible mechanism of the POD reaction is discussed on the basis of that of a known Fe(II)-dependent dioxygenase.

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The history of aerobic ammonia oxidizers: from the first discoveries to today

Cited by 65 publications

References 124 publications

Urea Hydrolysis Rate in Soil Toposequences as Influenced by pH, Carbon, Nitrogen, and Soluble Metals

Urea Hydrolysis Rate in Soil Toposequences as Influenced by pH, Carbon, Nitrogen, and Soluble Metals

The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

Pyruvic oxime dioxygenase from heterotrophic nitrifier Alcaligenes faecalis is a nonheme Fe(II)-dependent enzyme homologous to class II aldolase

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