Relative Contribution Of Ammonia-oxidizing Archaea Research Articles

Contributions of Ammonia-Oxidizing Archaea and Bacteria to Nitrous Oxide Production in Intensive Greenhouse Vegetable Fields

With excessive nitrogen (N) input, high nitrous oxide (N2O) emissions are frequently observed in greenhouse vegetable fields. We hypothesized that the underlying production mechanisms can be derived across a wide selection of vegetable fields in the middle and lower reaches of the Yangtze River. Thus, we investigated the emission characteristics and relative contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and other microbial processes to the N2O production from five long-term greenhouse vegetable fields through an incubation experiment with combined inhibition methods. The results showed that the ammonia oxidation process is the dominant contributor to N2O production at all five sites, accounting for 88–97% of the total N2O emissions. Regardless of acidic, neutral, or alkaline soil, AOA-driven N2O emission rates were consistently higher than AOB-driven N2O emission rates. Both AOA-driven and AOB-driven N2O emissions exhibited positive correlations with soil pH, with significant increases in soil N2O production associated with high pH levels. Therefore, general production mechanisms were derived, such that more attention should be paid to AOA-driven N2O emissions and to vegetable soils with a relatively high pH in the middle and lower reaches of the Yangtze River.

Different contributions of ammonia oxidizing archaea and bacteria to nitrification in soils amended with equivalent amounts of either ammonium-N or organic-N

Although considerable knowledge exists on the impact of crop residues on soil N availability, information about their impact on nitrification specifically is lacking. The unique physiologies of ammonia oxidizing archaea (AOA) suggests their activities might respond differently to crop residue amendment compared to ammonia oxidizing bacteria (AOB). An incubation study was conducted on two widely distributed Oregon agricultural silt loam soils of the Walla Walla (WW) and Woodburn (CC) series, amended with a fertilizer rate of 70 μg N g−1 soil in the form of (1) NH4+-N, (2) clover stems (C:N ~ 25), or (3) clover leaves (C:N ~ 13). NH4+ accumulation in the presence of acetylene, and the relative amounts of AOA and AOB activities, in the presence of the selective AOB inhibitor, 1-octyne, were examined over a 28-31d incubation. Nitrifying activity in the crop residue-amended WW soil matched the rate of ammonification and was predominately octyne-resistant suggesting that nitrifying activity was dominated by AOA. In CC soil, the relative contributions of AOA and AOB to emergent activities was influenced by the nature of the residue and in a soil specific manner. In leaf amended CC soil, AOB contributed the majority of initial nitrifying activity over 0-7d, with the contribution of AOA activity increasing post 7d to represent 100% of the total rate. In stem amended CC soil, emergence of nitrifying and ammonifying activities were delayed, but after 7d incubation AOA activity emerged at a rate greater than the accompanying rate of ammonification. In NH4+-N amended soils, AOB activity emerged quickly at rates greater than when N was supplied by residues. The response of AOA activity to NH4+-N was soil specific being immediate and at a greater rate than leaf residue supported activity in WW soil, whereas in CC soil, AOA activity was temporally delayed (as with residue treatment) and emerged at a rate similar to that supported by leaf residue. From a practical perspective, the findings of this study show that an application of 70 μg N g−1 soil as crop residues can prevent AOB driven nitrifying activity from reaching its potential compared to an inorganic NH4+-N application, and also suggest the potential of AOA activity to be modified by residues in a soil specific manner.

Dominance of archaeal ammonia-oxidizers in soil nitrification across different soil types and fertilities in North China plain

Microbially mediated soil nitrification process was largely limited by ammonia-oxidizing archaea (AOA) and bacteria (AOB), which further affect nitrogen (N) loss and retention with concomitant impacts on both crop productivity and environment. However, the spatial distribution of ammonia-oxidizers and their varying contributions to soil nitrification activity at provincial scale are poorly explored. 135 agricultural soils across different soil types and fertility conditions were collected from Henan province in North China Plain to draw the map of soil AOA and AOB abundance with quantitative PCR analysis. Soil nitrification potential (NP) and the relative contribution of AOA and AOB to NP that recovers after acetylene inactivation were essentially determined among the five major soil types. The abundance of ammonia-oxidizers, which was positively and significantly related with pH, was obviously predominated by AOA with AOA/AOB ranging 1.96–9.79 at provincial scale. AOA contributed more (at 60%–79%) to soil nitrification in acidic and neutral soils (Lime concretion black soil, Yellow-cinnamon soil, Paddy soil and Cinnamon soil) with significant relationships with its higher abundance, pH, soil organic carbon and ammonium nitrogen. On the contrary, the even contribution of AOB compared with AOA in alkaline Fulvo-aquic soil showed poor relationship with its abundance but was strongly affected by soil N availability. In summary, AOA even with lower abundance showed stronger function in acidic and ammonia-limited soil environments, but AOB with higher abundance tends to be the leader of soil nitrification in alkaline and substrate-rich soils of Henan province.

Molecular analysis of microbial nitrogen transformation and removal potential in mangrove wetlands under anthropogenic nitrogen input

Mangrove ecosystems are natural nitrogen removal systems that are primarily mediated by nitrogen cycle microorganisms, but their relative contributions to nitrogen transformation and removal in mangrove sediments under anthropogenic nitrogen input needs further resolution and characterization. Here, we investigated the responses and the relative contributions of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), anaerobic ammonium oxidizing (anammox) bacteria and denitrifying bacteria after spiking urea into mangrove sediments incubated in a laboratory microcosm experiment for four weeks. During incubation, the diversity, abundances and transcription levels of the hzo genes for anammox bacteria, amoA genes for AOA and AOB, and nirS genes for denitrifying bacteria were monitored using targeted gene clone library analyses and quantitative PCR assays at the DNA and RNA levels. The results showed that mangrove sediments harbour habitat-specific anammox bacteria which related to Candidatus Scalindua and Candidatus Kuenenia clades. Mangrove specific AOA related to deep branched clades within Candidatus Nitrososphaera and Candidatus Nitrosotalea, and AOB related to Nitrosomonas and Nitrosospira were also detected in the collected sediment samples. Growth and activity of AOA were detected at all levels of amendment of nitrogen input, whereas AOB growth was detectable only at the high-level nitrogen input (1.5 mg urea per gram of dry sediment) with no amoA transcripts and lower abundance than AOA. The abundance and transcription levels of the nirS gene were higher (~1000 times) than those of the hzo gene in all groups. Pearson correlation analysis demonstrated that the abundance of both AOA and AOB amoA genes had a significant positive correlation with the nirS gene (p < 0.01). These results indicated that nitrification (primarily mediated by the AOA)-denitrification process played the most important role in nitrogen removal from the amendment of nitrogen short-term input in the mangrove sediments.

Long-term mineral fertilizer substitution by organic fertilizer and the effect on the abundance and community structure of ammonia-oxidizing archaea and bacteria in paddy soil of south China

Ammonia oxidation in the soil is related to nitrogen (N) availability for plants, nitrate loss, and N fertilizer use efficiency, which is important for studies on the N cycle of paddy field ecosystems. Substitution of partial mineral N fertilizer with organic amendments is commonly considered to optimize fertilization practices and reduce the application of mineral N fertilizer in the paddy fields. However, little is known about the effects of this type of fertilization on the relative contribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to soil nitrification. Therefore, a 34-year field trial including five fertilization regimes (CK, without fertilizer; NPK, mineral NPK fertilizer; NPKM1, 70% inorganic N + 30% organic N + PK; NPKM2, 50% inorganic N + 50% organic N + PK; NPKM3, 30% inorganic N + 70% organic N + PK; P: phosphorus, K: potassium) was conducted. AOA and AOB abundance and community structures were determined by quantitative PCR and high-throughput sequencing analyses. Although the abundance of AOA and AOB increased with the increase in the percentage (30%–70%) of organic N substitution, the abundance ratio of AOA to AOB (133.9–84.7) decreased. Soil potential nitrification rate (PNR) increased dramatically (p < 0.05) after replacing chemical N with organic N, and with the increase in the substitution ratio of organic N in paddy soils. AOA and AOB both correlated significantly (p < 0.05) with PNR, but the contribution of AOB to PNR exceeded that of AOA. Soil carbon (C) to N ratio was the best predictor (43.0%) for AOA abundance, while total N and NH4+-N incorporating models were the best predictors (90.3%) for AOB abundance. Variations in AOA composition correlated strongly with fertilizer-induced changes in soil pH and ammonia concentration, whereas the AOB community was only markedly correlated with pH (p = 0.004). The substitution of 30%–70% of mineral N with organic N could increase the soil pH to 5.54–5.87, and that of ammonia concentration to 8.37–24.1 μM, which was the main reason that AOB contributed more to PNR than AOA. These results indicate that the organic substitution fertilizer regime had much stronger effects on the abundance and composition of AOB than AOA, and the potential contribution of AOB to ammonia oxidation in paddy soils should not be ignored after mineral N partial substitution by organic N.

Green manuring inhibits nitrification in a typical paddy soil by changing the contributions of ammonia-oxidizing archaea and bacteria

Rice–rice–green manure rotations in south China are characterized by high efficiency and good environmental performance, and the application of green manure plays an important role in N management. Nitrification is a key process in N cycling and is highly correlated with the N utilization of crops and with leaching losses. As a potential N loss pathway, the nitrification process and nitrifiers as affected by green manuring are of critical importance. A pot experiment covering green manure-double rice rotation was conducted to evaluate the effects of green manure and N fertilizer on soil nitrification and to achieve a mechanistic understanding of underlying processes in an alkaline paddy soil. Soil nitrification potential (NP) and the recovered nitrification potential (RNP) were measured. Relative contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in soil nitrification were studied using specific bacterial inhibitors. In the alkaline paddy soil, soil NP and nitrate concentrations were significantly decreased by green manuring but increased with increasing N fertilization. Soil nitrification was dominated by AOB and that the relative contributions of AOB to RNP ranged from 65% to 79% at different sampling stages despite the larger abundance of AOA amoA gene numbers. RNP and the contribution of AOB to RNP were significantly increased by N fertilizer, whereas the contribution of AOA was decreased by green manuring. We concluded that the application of inorganic N enhanced NP while green manures reduced it, which is consistent with the variation of observed soil nitrate concentrations. These results indicate that the utilization of winter green manure is an effective practice to improve N management in paddy rice.

High contribution of ammonia-oxidizing archaea (AOA) to ammonia oxidation related to a potential active AOA species in various arable land soils

Ammonia oxidation is the limiting step in soil nitrification and critical in the global nitrogen cycle. The discovery of ammonia-oxidizing archaea (AOA) has improved our knowledge of microbial mechanisms for ammonia oxidation in complex soil environments. However, the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation remain unclear. In this study, through large geographical scale sampling in China, totally nine samples representing various types of arable land soils were selected for analyzing the ammonia oxidation activity. The AOA and AOB activities were separately determined by using the dicyandiamide and 1-octyne inhibition method. High-throughput pyrosequencing and DNA stable-isotope probing (DNA-SIP) analysis were applied to investigate the distribution and activity of Candidatus Nitrosocosmicus franklandus in the arable land soils. In this study, AOA abundance (3.2 × 107–3.4 × 109 copies g−1) and activity (0.01–1.33 mg N kg−1 dry soil day−1) were evaluated for nine selected arable land soils and accounted for 4–100% of ammonia oxidation. By separately determining AOA and AOB rates, we observed that archaeal ammonia oxidation dominated the ammonia oxidation process in six soils, revealing a considerable contribution of AOA in ammonia oxidation in arable land soils. Based on high-throughput pyrosequencing analysis, the AOA species Ca. N. franklandus with relatively low abundance (0.6–13.5% in AOA) was ubiquitously distributed in all the tested samples. Moreover, according to the DNA-SIP analysis for Urumqi sample, the high activity and efficiency of Ca. N. franklandus in using CO2 suggests that this species plays an important role in archaeal ammonia oxidation in arable land soils. Through determining the AOA activity and analyzing the potential predominant functional AOA species, this study greatly improves our understanding of ammonia oxidation in arable land soils.

Distinct drivers of activity, abundance, diversity and composition of ammonia-oxidizers: evidence from a long-term field experiment

Ammonia oxidation, the primary and rate-limiting step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the dominant environmental driver of the activity, abundance, diversity and composition of ammonia-oxidizers has not been well understood enough, and the relative contribution of AOA and AOB to nitrification is still under debate. Soils treated with different fertilization regimes in an over 35-year field experiment were collected to explore the variation in function and structure of ammonia-oxidizer communities and corresponding driver. The highest nitrification activity (44.49 mg N kg−1 soil d−1) was found in only organic fertilizer (O) treated soil, whereas the lowest activity (2.81 mg N kg−1 soil d−1) was observed in only mineral fertilizer (NPK) treated soil. Moreover, as 1-octyne was employed to discriminate AOA- and AOB-supported nitrification, AOA dominated (93.53%) the nitrification in the Control soil, while AOB contributed dominantly (84.73–89.10%) in all of the organic amended soils, and NPK-treated soil showed an almost equal contribution to AOA (45.79%) and AOB (54.21%). Compared with the Control soil, AOA abundance increased in soils with organic and low chemical fertilizer but decreased in only chemically treated soil, whereas the AOB abundance in all fertilized soils was greatly enhanced. The AOA activity was linearly dependent on AOA abundance, whereas the AOB activity was exponentially correlated with AOB abundance. The sequences of AOA and AOB in the Control soil were mostly affiliated with group I.1b thaumarchaeota and genus Nitrosospira clusters 3a.1. Soil treated with NPK increased the abundance of AOA that belonged to group I.1a-associated lineage, whereas more abundant AOB was related to Nitrosospira clusters 3a.2 and 8b. In contrast, the O-treated soil showed more abundant AOB that belonged to Nitrosospira clusters 3b and 8b. As revealed by aggregated boosted tree analysis, the soil ammonium (NH4+) content was identified as the dominant driver of activity and diversity of AOA, and soil pH was considered to be the major influencing factor in abundance and composition of AOA; the AOB composition was mainly affected by soil NH4+ content, the relative activity and diversity by soil pH, and the relative abundance by soil electrical conductivity (EC). Collectively, different fertilization regimes will result in variations in activity, abundance, diversity and composition of ammonia-oxidizers with distinct drivers. Our research could be helpful to identify better strategies for the mitigation of nitrate production in agricultural soils.

Ammonia-Oxidizing Archaea Dominate Ammonia-Oxidizing Communities within Alkaline Cave Sediments

ABSTRACTNitrification represents one of the key steps in the global nitrogen cycle. While originally considered an exclusive metabolic capability of bacteria, the identification of the Thaumarchaeota revealed that ammonia-oxidizing archaea (AOA) are also important contributors to this process, particularly in acidic environments. Nonetheless, the relative contribution of AOA to global nitrification remains difficult to ascertain, particularly in underexplored neutrophilic and alkalinophilic terrestrial systems. In this study we examined the contribution of AOA to nitrification within alkaline (pH 8.3–8.7) cave environments using quantitative PCR, crenarchaeol lipid identification and measurement of potential nitrification rates. Our results showed that AOA outnumber ammonia-oxidizing bacteria (AOB) by up to four orders of magnitude in cave sediments. The dominance of Thaumarchaeota in the archaeal communities was confirmed by both archaeal 16S rRNA gene clone library and membrane lipid analyses, while potential nitrification rates suggest that Thaumarchaeota may contribute up to 100% of ammonia oxidation in these sediments. Phylogenetic analysis of Thaumarchaeota amoA gene sequences demonstrated similarity to amoA clones across a range of terrestrial habitats, including acidic ecosystems. These data suggest that despite the alkaline conditions within the cave, the low NH3 concentrations measured continue to favor growth of AOA over AOB populations. In addition to providing important information regarding niche differentiation within Thaumarchaeota, these data may provide important clues as to the factors that have historically led to nitrate accumulation within cave sediments.

Archaeal Ammonia Oxidizers Dominate in Numbers, but Bacteria Drive Gross Nitrification in N-amended Grassland Soil.

Both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium, or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.

Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA- and AOB-supported nitrification determined both in soil-water slurries and in unsaturated whole soil at field moisture. Soils were collected from stands of red alder (Alnus rubra Bong.) and Douglas-fir (Pseudotsuga menziesii Mirb. Franco) at three sites (Cascade Head, the H.J. Andrews, and McDonald Forest) on acidic soils (pH 3.9–5.7) in Oregon, USA. The abundances of AOA and AOB were measured using quantitative PCR by targeting the amoA gene, which encodes subunit A of ammonia monooxygenase. Total and AOA-specific (octyne-resistant) nitrification activities in soil slurries were significantly higher at Cascade Head (the most acidic soils, pH < 5) than at either the H.J. Andrews or McDonald Forest, and greater in red alder compared with Douglas-fir soils. The fraction of octyne-resistant nitrification varied among sites (21–74%) and was highest at Cascade Head than at the other two locations. Net nitrification rates of whole soil without NH4+ amendment ranged from 0.4 to 3.3 mg N kg−1 soil d−1. Overall, net nitrification rates of whole soil were stimulated 2- to 8-fold by addition of 140 mg NH4+-N kg−1 soil; this was significant for red alder at Cascade Head and the H.J. Andrews. Red alder at Cascade Head was unique in that the majority of NH4+-stimulated nitrifying activity was octyne-resistant (73%). At all other sites, NH4+-stimulated nitrification was octyne-sensitive (68–90%). The octyne-sensitive activity—presumably AOB—was affected more by soil pH whereas the octyne-resistant (AOA) activity was more strongly related to N availability.

Cycloheximide prevents thede novopolypeptide synthesis required to recover from acetylene inhibition inNitrosopumilus maritimus

Developing methods to differentiate the relative contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to ammonia (NH3) oxidation has been challenging due to the lack of compounds that selectively inhibit AOA. In this study, we investigated the effects of specific bacteria- and eukaryote-selective protein synthesis inhibitors on the recovery of acetylene (C2H2)-inactivated NH3 oxidation in the marine AOA Nitrosopumilus maritimus and compared the results with recovery of the AOB Nitrosomonas europaea. C2 H2 irreversibly inhibited N. maritimus NH3 oxidation in a similar manner to what was observed previously with N. europaea. However, cycloheximide (CHX), a widely used eukaryotic protein synthesis inhibitor, but not bacteria-specific protein synthesis inhibitors (kanamycin and gentamycin), inhibited the recovery of NH3-oxidizing activity in N. maritimus. CHX prevented the incorporation of (14)CO2 -labeling into cellular proteins, providing further evidence that CHX acts as a protein synthesis inhibitor in N. maritimus. If the effect of CHX on protein synthesis can be confirmed among other isolates of AOA, the combination of C2H2 inactivation followed by recovery of NH3 oxidation either in the presence of bacteria-selective protein synthesis inhibitors or CHX might be used to estimate the relative contributions of AOB and AOA to NH3 oxidation in natural environments.

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

Increasing evidence demonstrated the involvement of ammonia-oxidizing archaea (AOA) in the global nitrogen cycle, but the relative contributions of AOA and ammonia-oxidizing bacteria (AOB) to ammonia oxidation are still in debate. Previous studies suggest that AOA would be more adapted to ammonia-limited oligotrophic conditions, which seems to be favored by protonation of ammonia, turning into ammonium in low-pH environments. Here, we investigated the autotrophic nitrification activity of AOA and AOB in five strongly acidic soils (pH<4.50) during microcosm incubation for 30 days. Significantly positive correlations between nitrate concentration and amoA gene abundance of AOA, but not of AOB, were observed during the active nitrification. (13)CO(2)-DNA-stable isotope probing results showed significant assimilation of (13)C-labeled carbon source into the amoA gene of AOA, but not of AOB, in one of the selected soil samples. High levels of thaumarchaeal amoA gene abundance were observed during the active nitrification, coupled with increasing intensity of two denaturing gradient gel electrophoresis bands for specific thaumarchaeal community. Addition of the nitrification inhibitor dicyandiamide (DCD) completely inhibited the nitrification activity and CO(2) fixation by AOA, accompanied by decreasing thaumarchaeal amoA gene abundance. Bacterial amoA gene abundance decreased in all microcosms irrespective of DCD addition, and mostly showed no correlation with nitrate concentrations. Phylogenetic analysis of thaumarchaeal amoA gene and 16S rRNA gene revealed active (13)CO(2)-labeled AOA belonged to groups 1.1a-associated and 1.1b. Taken together, these results provided strong evidence that AOA have a more important role than AOB in autotrophic ammonia oxidation in strongly acidic soils.

Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting

The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R2=0.554; P<0.001), indicating that archaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R2=0.503; P=0.03) especially during the mesophilic and maturation stages.