Bacterial Ammonia Oxidizers Research Articles

Contribution of ammonia-oxidizing archaea and ammonia-oxidizing bacteria to ammonia oxidation in two nitrifying reactors.

In this study, two laboratory nitrifying reactors (NRI and NRII), which were seeded by sludge from different sources and operated under different operating conditions, were found to possess distinct dominant ammonia-oxidizing microorganisms. Ammonia-oxidizing archaeal (AOA) amoA genes outnumbered ammonia-oxidizing bacterial (AOB) amoA genes in reactor NRI, while only AOB amoA genes were detectable in reactor NRII. The AOA amoA gene sequences retrieved from NRI were characterized within the Nitrososphaera sister cluster of the group 1.1b Thaumarchaeota. Two inhibitors for ammonia oxidation, allylthiourea (ATU) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), were applied individually and as a mixture to observe the ammonia-oxidizing activity of both microorganisms in the reactors' sludge. The results indicated that AOA and AOB jointly oxidized ammonia in NRI, while AOB played the main role in ammonia oxidation in NRII. DNA-stable isotope probing with labeled 13C-HCO3- was performed on NRI sludge. Incorporation of 13C into AOA and AOB implied that both microorganisms may perform autotrophy during ammonia oxidation. Taken together, the results from this study provide direct evidence demonstrating the contribution of AOA and AOB to ammonia oxidation in the nitrifying reactors.

Changes in nitrogen-cycling microbial communities with depth in temperate and subtropical forest soils

The soil nitrogen (N) cycle, as a network of interlinked processes, is mainly driven by microbial communities. However, the patterns and factors that influence the abundance of the different N-cycling microbial communities in temperate and subtropical forest soils are still poorly understood. Moreover, recent studies have tended to focus on surface soils, and have neglected the fact that there may be steep gradients in nutrient concentrations in forest soil profiles. The objective of our study was to determine whether the distributions and compositions of N-cycling microbial communities changed with depth in subtropical and temperate forest soils. We collected soil samples from the surface to 80cm deep from 2 forests, a native conifer mixed broadleaf temperate forest in northeast China and a native evergreen broadleaf subtropical forest in south eastern China. We used high-throughput sequencing to fingerprint the soil microbial community structures and real-time quantitative PCR to measure the abundances of N-cycling functional genes (NFGs), specifically those involved in organic N decomposition (chiA), N fixation (nifH), archaeal and bacterial ammonia oxidation (amoA; AOA and AOB, respectively), and nitrite reduction (nirK and nirS). The composition and diversity of N-cycling microbes shifted between the upper and lower soils. Because of changes in soil nutrient concentrations and soil conditions with soil depth, N-cycling microbial taxa searched for different ecological niches. The absolute abundances of NFGs decreased with depth in both forest soils, indicating that N transformations mainly occurred in surface soil. The relative abundances of NFGs differed between the two forest soils. Because the soil C/N ratios declined with depth in the soil profile, N-cycling microbes invested less energy in N-supplying mineralization and fixation processes that were C-intensive and invested more energy in ammonia oxidization to balance the soil stoichiometry in the subtropical forest subsoils. The nifH, which dominated the soil profiles of the temperate forest were mainly controlled by the soil N concentrations, indicating the high microbial demand for N. We also found that the microbial N storage potentials were lower, and the NO3−-N leaching potentials were higher, in the N-rich subtropical forest surface soils and subsoils than in the temperate forest subsoils and surface soils, and that these potentials were significantly correlated with the soil N/P ratios. This suggests that N-cycling microbes change their energy investments at the molecular scale depending on the level of N saturation in the soil.

Dimethyl pyrazol-based nitrification inhibitors effect on nitrifying and denitrifying bacteria to mitigate N2O emission

Nitrous oxide (N2O) emissions have been increasing as a result of intensive nitrogen (N) fertilisation. Soil nitrification and denitrification are the main sources of N2O, and the use of ammonium-based fertilisers combined with nitrification inhibitors (NIs) could be useful in mitigating N2O emissions from agricultural systems. In this work we looked at the N2O mitigation capacity of two dimethylpyrazol-based NIs, 3,4-dimethylpyrazole phosphate (DMPP) and 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture (DMPSA), on soil nitrifying and denitrifying microbial populations under two contrasting soil water contents (40% and 80% soil water filled pore space; WFPS). Our results show that DMPP and DMPSA are equally efficient at reducing N2O emissions under 40% WFPS conditions by inhibiting bacterial ammonia oxidation. In contrast, at 80% WFPS DMPSA was less efficient than DMPP at reducing N2O emissions. Interestingly, at 80% WFPS, where lowered oxygen availability limits nitrification, both DMPP and DMPSA not only inhibited nitrification but also stimulated N2O reduction to molecular nitrogen (N2) via nitrous oxide reductase activity (Nos activity). Therefore, in this work we observed that DMP-based NIs stimulated the reduction of N2O to N2 by nitrous oxide reductase during the denitrification process.

Soil Conditions Rather Than Long-Term Exposure to Elevated CO2 Affect Soil Microbial Communities Associated with N-Cycling.

Continuously rising atmospheric CO2 concentrations may lead to an increased transfer of organic C from plants to the soil through rhizodeposition and may affect the interaction between the C- and N-cycle. For instance, fumigation of soils with elevated CO2 (eCO2) concentrations (20% higher compared to current atmospheric concentrations) at the Giessen Free-Air Carbon Dioxide Enrichment (GiFACE) sites resulted in a more than 2-fold increase of long-term N2O emissions and an increase in dissimilatory reduction of nitrate compared to ambient CO2 (aCO2). We hypothesized that the observed differences in soil functioning were based on differences in the abundance and composition of microbial communities in general and especially of those which are responsible for N-transformations in soil. We also expected eCO2 effects on soil parameters, such as on nitrate as previously reported. To explore the impact of long-term eCO2 on soil microbial communities, we applied a molecular approach (qPCR, T-RFLP, and 454 pyrosequencing). Microbial groups were analyzed in soil of three sets of two FACE plots (three replicate samples from each plot), which were fumigated with eCO2 and aCO2, respectively. N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers producing ammonia were targeted by analysis of functional marker genes, and the overall archaeal community by 16S rRNA genes. Remarkably, soil parameters as well as the abundance and composition of microbial communities in the top soil under eCO2 differed only slightly from soil under aCO2. Wherever differences in microbial community abundance and composition were detected, they were not linked to CO2 level but rather determined by differences in soil parameters (e.g., soil moisture content) due to the localization of the GiFACE sets in the experimental field. We concluded that +20% eCO2 had little to no effect on the overall microbial community involved in N-cycling in the soil but that spatial heterogeneity over extended periods had shaped microbial communities at particular sites in the field. Hence, microbial community composition and abundance alone cannot explain the functional differences leading to higher N2O emissions under eCO2 and future studies should aim at exploring the active members of the soil microbial community.

Overall bacterial community composition and abundance of nitrifiers and denitrifiers in a typical macrotidal estuary

Coupled nitrogen cycling processes can alleviate the negative effects of eutrophication caused by excessive nitrogen load in estuarine ecosystems. The abundance and diversity of nitrifiers and denitrifiers across different environmental gradients were examined in the sediment of Hangzhou Bay. Quantitative PCR and Pearson's correlation analyses suggested that the bacterial ammonia-oxidizers (AOB) were the dominant phylotypes capable of ammonia oxidation, while the nirS-encoding denitrifiers predominated in the denitrification process. Simultaneously, nitrite and pH were found to be the two major factors influencing amoA and nir gene abundances, and the distribution of bacterial communities. Moreover, the ratio of nirS/AOB amoA gene abundance showed negative correlation with nitrite concentration. Fluorescence in situ hybridization further demonstrated that AOB and acetate-denitrifying cells were closely connected and formed obvious aggregates in the sediment. Together, all these results provided us a preliminary insight for coupled nitrification-denitrification processes in the sediment of Hangzhou Bay.

Soil pH and plant diversity drive co-occurrence patterns of ammonia and nitrite oxidizer in soils from forest ecosystems

In this study, we investigated how co-occurrence patters of ammonia and nitrite oxidizers, which drive autotrophic nitrification, are influenced by tree species composition as well as soil pH in different forest soils. We expected that a decline of ammonia oxidizers in coniferous forests, as a result of excreted nitrification inhibitors and at acidic sites with low availability of ammonia, would reduce the abundance of nitrite-oxidizing bacteria (NOB). To detect shifts in co-occurrence patterns, the abundance of key players was measured at 50 forest plots with coniferous respectively deciduous vegetation and different soil pH levels in the region Schwabische Alb (Germany). We found ammonia-oxidizing archaea (AOA) and Nitrospira-like NOB (NS) to be dominating in numbers over their counterparts across all forest types. AOA co-occurred mostly with NS, while bacterial ammonia oxidizers (AOB) were correlated with Nitrobacter-like NOB (NB). Co-occurrence patterns changed from tight significant relationships of all ammonia and nitrite oxidizers in deciduous forests to a significant relationship of AOB and NB in coniferous forests, where AOA abundance was reduced. Surprisingly, no co-occurrence structures between ammonia and nitrite oxidizers could be determined at acidic sites, although abundances were correlated to the respective nitrogen pools. This raises the question whether interactions with heterotrophic nitrifiers may occur, which needs to be addressed in future studies.

Day–night ammonium oxidation in an urban stream: the influence of irradiance on ammonia oxidizers

Efficient NH4+ oxidation is a critical issue in human-impaired streams receiving high N loads from the effluent of wastewater treatment plants (WWTP). Archaeal (AOA) and bacterial (AOB) ammonia oxidizers are strongly photoinhibited in laboratory cultures, so we expected that light availability would affect the distribution of AOA and AOB and NH4+ oxidation rates at the reach scale. We selected 2 contiguous reaches downstream of a WWTP input in La Tordera river (northeastern Spain) that strongly differed in canopy cover (open and shaded). Against expectations and despite significant differences in light availability, the 2 reaches showed similar abundance of AOA and AOB and similar daily rates of ecosystem respiration, gross primary productivity, and NH4+ oxidation. The abundance of ammonia oxidizers was not correlated with biomass in biofilms protected from light, whereas a positive relationship was found for light-exposed biofilms. This result suggests that biomass accrual could provide light protection to ammonia oxidizers in light-exposed biofilms. The contribution of NH4+ oxidation to whole-reach NH4+ uptake reached up to 89%, indicating a high potential for NH4+ oxidation in the 2 reaches. NH4+ oxidation rates were similar between night and day, but their contribution to whole-reach NH4+ uptake tended to be higher at night than during the day. Altogether, these findings highlight that environmental factors other than irradiance drive reach-scale NH4+ oxidation in this urban stream.

Relative contribution of ammonia oxidizing bacteria and other members of nitrifying activated sludge communities to micropollutant biotransformation

Improved micropollutant (MP) biotransformation during biological wastewater treatment has been associated with high ammonia oxidation activities, suggesting co-metabolic biotransformation by ammonia oxidizing bacteria as an underlying mechanism. The goal of this study was to clarify the contribution of ammonia oxidizing bacteria to increased MP degradation in nitrifying activated sludge (NAS) communities using a series of inhibition experiments. To this end, we treated a NAS community with two different ammonia oxidation inhibitors, namely octyne (OCT), a mechanistic inhibitor that covalently binds to ammonia monooxygenases, and allylthiourea (ATU), a copper chelator that depletes copper ions from the active center of ammonia monooxygenases. We investigated the biotransformation of 79 structurally different MPs by the inhibitor-treated and untreated sludge communities. Fifty-five compounds exhibited over 20% removal in the untreated control after a 46 h-incubation. Of these, 31 compounds were significantly inhibited by either ATU and/or OCT. For 17 of the 31 MPs, the inhibition by ATU at 46 h was substantially higher than by OCT despite the full inhibition of ammonia oxidation by both inhibitors. This was particularly the case for almost all thioether and phenylurea compounds tested, suggesting that in nitrifying activated sludge communities, ATU does not exclusively act as an inhibitor of bacterial ammonia oxidation. Rather, ATU also inhibited enzymes contributing to MP biotransformation but not to bulk ammonia oxidation. Thus, inhibition studies with ATU tend to overestimate the contribution of ammonia-oxidizing bacteria to MP biotransformation in nitrifying activated sludge communities. Biolog tests revealed only minor effects of ATU on the heterotrophic respiration of common organic substrates by the sludge community, suggesting that ATU did not affect enzymes that were essential in energy conservation and central metabolism of heterotrophs. By comparing ATU- and OCT-treated samples, as well as before and after ammonia oxidation was recovered in OCT-treated samples, we were able to demonstrate that ammonia-oxidizing bacteria were highly involved in the biotransformation of four compounds: asulam, clomazone, monuron and trimethoprim.

Stream drying drives microbial ammonia oxidation and first-flush nitrate export.

Stream microbial communities and associated processes are influenced by environmental fluctuations that may ultimately dictate nutrient export. Discharge fluctuations caused by intermittent stream flow are increasing worldwide in response to global change. We examined the impact of flow cessation and drying on in-stream nitrogen cycling. We determined archaeal (AOA) and bacterial ammonia oxidizer (AOB) abundance and ammonia oxidation activity in surface and deep sediments from different sites along the Fuirosos stream (Spain) subjected to contrasting hydrological conditions (i.e., running water, isolated pools, and dry streambeds). AOA were more abundant than AOB, with no major changes across hydrological conditions or sediment layers. However, ammonia oxidation activity and sediment nitrate content increased with the degree of stream drying, especially in surface sediments. Upscaling of our results shows that ammonia oxidation in dry streambeds can contribute considerably (~50%) to the high nitrate export typically observed in intermittent streams during first-flush events following flow reconnection. Our study illustrates how the dry channels of intermittent streams can be potential hotspots of ammonia oxidation. Consequently, shifts in the duration, spatial extent and severity of intermittent flow can play a decisive role in shaping nitrogen cycling and export along fluvial networks in response to global change.

Soil texture modulates the response of ammonia-oxidizing prokaryotes to biochemical quality of organic inputs in tropical agricultural soils

Soil texture modulates the response of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities to biochemical quality of organic inputs in tropical agricultural soils. To verify this assumption, we used the soil organic matter long-term field experiments in Kenya established on contrasting soils (i.e., clayey Humic Nitisol, sandy Ferric Alisol) in 2002. Since the start of the experiments, soils were continuously treated (4 Mg C ha−1 year−1) with biochemically different organic inputs including Tithonia diversifolia (TD; C/N ratio: 13, Lignin: 8.9%; Polyphenols: 1.7%), Calliandra calothyrsus (CC; 13; 13; 9.4) and Zea mays stover (ZM; 59; 5.4; 1.2). In 2013, soils (0–15 cm) were sampled at young growth (EC30) and flowering (EC60) stages of maize and subjected to DNA-based community analysis of AOB, AOA and 16S rRNA genes. Soil texture exerted stronger effects on the dynamics of the assayed genes than organic input quality with AOB being more responsive than AOA. Clayey soil with its predominant soil organic matter background and large surface area of clay minerals revealed generally higher AOB and AOA abundance than the sandy soil. In the sandy soil, N-rich TD and cellulose-rich ZM promoted AOB abundance, while it was decreased under CC due to N limitation induced by high contents of polyphenols and lignin. N limitation under ZM revealed a clear community differentiation of AOB between ZM versus TD and CC in the clayey soil. For the sandy soil, AOA community composition was distinct between CC versus TD and ZM. To provide a more detailed mechanistic understanding of active AOB and AOA in response to organic input quality, we recommend for prospective research RNA-based along with enzymatic analyses as complement to those shown in this study. This should be approached using controlled experiments to eliminate interfering environmental effects including rainfall and soil moisture, respectively.

Ammonia half-saturation constants of sludge with different community compositions of ammonia-oxidizing bacteria

Owing to the kinetic differences in ammonia oxidation among ammonia-oxidizing microorganisms (AOM), there is no standard set of kinetic values that can be used as a representative set for nitrifying wastewater treatment plant (WWTP) design. As a result, this study clarified a link between the half-saturation constants for ammonia oxidation (Ks) and the dominant ammonia-oxidizing bacterial (AOB) groups in sludge from full-scale WWTPs and laboratory-scale nitrifying reactors. Quantitative polymerase chain reaction analyses revealed that AOB affiliated with the Nitrosomonas oligotropha cluster were the dominant AOM groups in the sludge taken from the low-ammonia-level WWTPs, while AOB associate with the Nitrosomonas europaea cluster comprised the majority of AOM groups in the sludge taken from the high-ammonia-level WWTPs and nitrifying reactors. A respirometric assay demonstrated that the ammonia Ks values for the high-ammonia- level WWTPs and nitrifying reactors were higher than those of the low-ammonia-level plants. Using the Ks values of available AOM cultures as a reference, the Ks values of the analyzed sludge were mainly influenced by the dominant AOB species. These findings implied that.different sets of kinetic values may be required for WWTPs with different dominant AOM species for more accurate WWTP design and operations.

Autotrophic nitrogen removal in membrane-aerated biofilms: Archaeal ammonia oxidation versus bacterial ammonia oxidation

Recent discovery of ammonia-oxidizing archaea (AOA) not only substantially improved our understanding of the global nitrogen cycle, but also provided new possibilities for nitrogen removal from wastewater. In particular, compared to ammonia-oxidizing bacteria (AOB), the high ammonia oxidation under oxygen-limited conditions driven by AOA is potentially more suitable for autotrophic nitrogen removal in a single-stage membrane aerated biofilm reactor (MABR) through coupling with anaerobic ammonia oxidation (Anammox). In this work, mathematical modeling is applied to assess the system performance and associated microbial community structure of an AOA–Anammox MABR under low- (30mgNL−1) and high-strength (500mgNL−1) ammonium conditions, with a side-by-side comparison to an AOB–Anammox MABR system under the same conditions. Results demonstrate that both ammonium surface loading (or hydraulic retention time) and oxygen surface loading significantly affect the system performance. In contrast to AOB–Anammox system, the AOA–Anammox MABR shows higher total nitrogen (TN) removal and lower oxygen supply, with much better repression of NOB and substantially wider operating window for high-level TN removal (>80%) in terms of varied oxygen and ammonium loadings. These results provide first insights and useful information for design and operation of this novel AOA–Anammox MABR system in its potential future applications.

Archaea produce lower yields of N2 O than bacteria during aerobic ammonia oxidation in soil.

Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N2 O), which is generated during denitrification and, in oxic soils, mainly by ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N2 O, their relative activities in soil are unknown. This work tested the hypothesis that AOB dominate ammonia oxidation and N2 O production under conditions of high inorganic ammonia (NH3 ) input, but result mainly from the activity of AOA when NH3 is derived from mineralisation. 1-octyne, a recently discovered inhibitor of AOB, was used to distinguish N2 O production resulting from archaeal and bacterial ammonia oxidation in soil microcosms, and specifically inhibited AOB growth, activity and N2 O production. In unamended soils, ammonia oxidation and N2 O production were lower and resulted mainly from ammonia oxidation by AOA. The AOA N2 O yield relative to nitrite produced was half that of AOB, likely due to additional enzymatic mechanisms in the latter, but ammonia oxidation and N2 O production were directly linked in all treatments. Relative contributions of AOA and AOB to N2 O production, therefore, reflect their respective contributions to ammonia oxidation. These results suggest potential mitigation strategies for N2 O emissions from fertilised agricultural soils.

Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance.

The influence of plants on archaeal (AOA) and bacterial (AOB) ammonia oxidisers (AO) is poorly understood. Higher microbial activity in the rhizosphere, including organic nitrogen (N) mineralisation, may stimulate both groups, while ammonia uptake by plants may favour AOA, considered to prefer lower ammonia concentration. We therefore hypothesised (i) higher AOA and AOB abundances in the rhizosphere than bulk soil and (ii) that AOA are favoured over AOB in the rhizosphere of plants with an exploitative strategy and high N demand, especially (iii) during early growth, when plant N uptake is higher. These hypotheses were tested by growing 20 grassland plants, covering a spectrum of resource-use strategies, and determining AOA and AOB amoA gene abundances, rhizosphere and bulk soil characteristics and plant functional traits. Joint Bayesian mixed models indicated no increase in AO in the rhizosphere, but revealed that AOA were more abundant in the rhizosphere of exploitative plants, mostly grasses, and less abundant under conservative plants. In contrast, AOB abundance in the rhizosphere and bulk soil depended on pH, rather than plant traits. These findings provide a mechanistic basis for plant-ammonia oxidiser interactions and for links between plant functional traits and ammonia oxidiser ecology.

Nitrogen removal performance and ammonia- and nitrite-oxidizing bacterial community analysis of a novel industrial waste-based biofilter

This study employed a newly developed treatment biofilter to remove high nitrogen (N) concentration from synthetic livestock wastewater combined with media containing neutralized used acid (NUA) and dewatered alum sludge (DAS). This biofilter was also utilized to investigate the spatial and temporal distributions of ammonia-oxidizing bacterial (AOB) and nitrite-oxidizing bacterial (NOB) communities and their active responses to effluent characteristics. Data were obtained from 210days of operations. Results showed that N removal was robust, with ammonia N and total N removal efficiencies of 59.8–82.1% and 57.5–74.9%, respectively. Denaturing gradient gel electrophoresis and sequence analyses revealed that the shift of AOB and NOB community structures in DAS was time dependent. These structures did not exhibit distinct differences in both media as depth varied. The retrieved AOB and NOB sequences from both media primarily belonged to Nitrosomonas, Nitrosovibrio, and Nitrobacter. The nitrification rates indicated that the change in AOB activity corresponded to the AOB community structure variation in the system. The peak was observed in DAS at the final time. By contrast, the NOB activity was inconsistent with the trend of its community structure. The AOB rate was positively related to the NOB rate. This finding suggested that AOB and NOB mutually promoted each other. The AOB and NOB activities of DAS rather than those of NUA appeared dependent on available nitrate from the effluent. Overall, these findings on AOB and NOB helped enhance further understanding on the efficient N removal of the NUA–DAS system.

Nitrification of archaeal ammonia oxidizers in a high- temperature hot spring

Abstract. The oxidation of ammonia by microbes has been shown to occur in diverse natural environments. However, the link of in situ nitrification activity to taxonomic identities of ammonia oxidizers in high-temperature environments remains poorly understood. Here, we studied in situ ammonia oxidation rates and the diversity of ammonia-oxidizing Archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3− pool dilution technique in the surface and bottom sediments were 4.80 and 5.30 nmol N g−1 h−1, respectively. Real-time quantitative polymerase chain reaction (qPCR) indicated that the archaeal 16S rRNA genes and amoA genes were present in the range of 0.128 to 1.96 × 108 and 2.75 to 9.80 × 105 gene copies g−1 sediment, respectively, while bacterial amoA was not detected. Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic Candidatus Nitrosocaldus yellowstonii, which represented the most abundant operational taxonomic units (OTU) in both surface and bottom sediments. The archaeal predominance was further supported by fluorescence in situ hybridization (FISH) visualization. The cell-specific rate of ammonia oxidation was estimated to range from 0.410 to 0.790 fmol N archaeal cell−1 h−1, higher than those in the two US Great Basin hot springs. These results suggest the importance of archaeal rather than bacterial ammonia oxidation in driving the nitrogen cycle in terrestrial geothermal environments.

Dynamics of bacterial and archaeal amoA gene abundance after additions of organic inputs combined with mineral nitrogen to an agricultural soil

Dynamics of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) abundance was assayed in a tropical Humic Nitisol during two cropping seasons of a long-term field experiment situated in the central highlands of Kenya. Since 2002, soils were treated yearly with biochemically contrasting organic inputs (4 Mg C ha−1 year−1) of Tithonia diversifolia (TD; C/N ratio: 13; lignin: 8.9 %; polyphenols: 1.7 %), Calliandra calothyrsus (CC; 13; 13; 9.4) and Zea mays (ZM; 59; 5.4; 1.2) combined with and without 120 kg CaNH4NO3 ha−1 season−1. In 2012 and 2013, soils (0–15 cm) were sampled at young growth (EC30) and flowering (EC60) stages of maize and subjected to DNA-based amoA gene quantification. ZM and TD increased AOB abundance by 9 and 19 %, respectively, compared to CC, while AOA remained unaffected. This was ascribed to high organic N in TD and lower lignin and polyphenol contents in ZM than in CC. In CC, formation of polyphenol-protein complexes limited microbial access to N. Sole use of mineral N or its combination with organic inputs decreased AOA abundance by 35 % but not AOB as a consequence of pH reduction by mineral N. Overall, AOB was more responsive than AOA to input quality that became most pronounced under optimal soil moisture conditions found in 2013 and at EC60 in 2012. We recommend prolonged study periods, considering also rRNA-based analyses to explore the dynamics of active nitrifying communities as a consequence of interrelations of contrasting organic inputs, crop growth stages and seasonality in agricultural soils.

Ammonia-oxidizing bacterial communities and shaping factors with different Phanerochaete chrysosporium inoculation regimes during agricultural waste composting

This research was conducted to determine the effects ofPhanerochaete chrysosporiuminoculation on the ammonia-oxidizing bacterial (AOB) communities during agricultural waste composting.

The effect of soil type, rice cultivar and water management on ammonia-oxidizing archaea and bacteria populations

Ammonia-oxidizing microorganisms are partly responsible for the production of N2O, a potent greenhouse gas. Rice paddies provide a habitat where ammonia oxidizing microorganisms can be active. The influence of different agricultural practices on these microorganisms, particularly on archaeal ammonia oxidizers, is an active field of research. In this work, we conducted two greenhouse experiments where we analyzed the influence of two soil types with different organic matter contents, two rice cultivars and water management on both archaeal (AOA) and bacterial (AOB) ammonia oxidizers. We determined the AOA and AOB abundance and population structure by q-PCR and T-RFLP, respectively. The archaeal and bacterial ammonia monooxygenase subunit A gene was used as the PCR target. The AOA and AOB copy numbers were affected by sampling time in both experiments. AOA abundance was also influenced by the time of flooding. The population structure of AOA was more variable than that of AOB and was strongly determined by soil type. Changes in AOB population structure were observed mainly according to sampling time.

Ammonia and nitrite oxidation in the Eastern Tropical North Pacific

AbstractNitrification plays a key role in the marine nitrogen (N) cycle, including in oceanic oxygen minimum zones (OMZs), which are hot spots for denitrification and anaerobic ammonia oxidation (anammox). Recent evidence suggests that nitrification links the source (remineralized organic matter) and sink (denitrification and anammox) of fixed N directly in the steep oxycline in the OMZs. We performed shipboard incubations with 15N tracers to characterize the depth distribution of nitrification in the Eastern Tropical North Pacific (ETNP). Additional experiments were conducted to investigate photoinhibition. Allylthiourea (ATU) was used to distinguish the contribution of archaeal and bacterial ammonia oxidation. The abundance of archaeal and β‐proteobacterial ammonia monooxygenase gene subunit A (amoA) was determined by quantitative polymerase chain reaction. The rates of ammonia and nitrite oxidation showed distinct subsurface maxima, with the latter slightly deeper than the former. The ammonia oxidation maximum coincided with the primary nitrite concentration maximum, archaeal amoA gene maximum, and the subsurface nitrous oxide maximum. Negligible rates of ammonia oxidation were found at anoxic depths, where high rates of nitrite oxidation were measured. Archaeal amoA gene abundance was generally 1 to 2 orders of magnitude higher than bacterial amoA gene abundance, and inhibition of ammonia‐oxidizing bacteria with 10 μM ATU did not affect ammonia oxidation rates, indicating the dominance of archaea in ammonia oxidation. These results depict highly dynamic activities of ammonia and nitrite oxidation in the oxycline of the ETNP OMZ.