Active Ammonia-oxidizing Archaea Research Articles

Nanoparticles of Zinc Oxides Mitigated N2O Emissions in Tea Plantation Soil

The excessive application of nitrogen in tea plantations leads to severe soil acidification and N2O emission boosting. To promote sustainable agriculture, nanoparticles (NPs) have emerged as alternative fertilizers, but their effects on soil nitrification and greenhouse gas emissions in tea plantations remain unclear. In this study, the effects of NP type (ZnO-NPs and Fe2O3-NPs) and dose (0, 1, 10, and 100 mg·kg−1) on soil N2O emissions were investigated via a lab incubation trial. Soil pH, ammonium, and nitrate changes were also monitored during the incubation period. The abundance of functional genes related to nitrification and denitrification processes was analyzed as well. The results showed that ZnO-NPs led to a decrease in N2O emissions. The reduction effect was stronger with increasing dose and resulted in a 33% reduction at an addition rate of 100 mg·kg−1. The cumulative N2O emissions had significantly positive correlations with NH4+-N and NO3−-N. ZnO-NP addition showed a significantly negative effect on Ammonia-Oxidizing Archaea (AOA) but a positive effect on Ammonia-Oxidizing Bacteria (AOB) gene abundance. In contrast, Fe2O3-NPs showed an insignificant impact on N2O emissions and soil N content, as well as nitrification–denitrification gene abundance, regardless of different doses. These results imply that the application of ZnO-NPs may inhibit nitrification through the retarding of AOA activity. This study provided us with a potential practice to reduce N2O emissions in tea plantations by applying ZnO-NPs, but the efficiency of this reduction needs further examination under ambient conditions before field application.

Impact of salinity and organic matter on the ammonia-oxidizing archaea and bacteria in treating hypersaline industrial wastewater: amoA gene abundance and ammonia removal contributions.

Studies publishedrecently proposed that ammonia-oxidizing archaea (AOA) may bebeneficial for hypersaline (salinity > 50g NaCl L-1) industrial wastewater treatment. However, knowledge of AOA activity in hypersaline bioreactors is limited. This study investigated the effects of salinity, organic matter, and practical pickled mustard tuber wastewater (PMTW) on AOA and ammonia-oxidizing bacteria (AOB) in two sequencing batch biofilm reactors (SBBRs). Results showed that despite observed salinity inhibition (p < 0.05), both AOA and AOB contributed to high ammonia removal efficiency at a salinity of 70 g NaCl L-1 in the two SBBRs. The ammonia removal efficiency of SBBR2 did not significantly differ from that of SBBR1 in the absence of organic matter (p > 0.05). Batch tests and quantitative real-time PCR (qPCR) reveal that salinity and organic matter inhibition resulted in a sharp decline in specific ammonia oxidation rates and amoA gene copy numbers of AOA and AOB (p < 0.05). AOA demonstrated higher abundance and more active ammonia oxidation activity in hypersaline and high organic matter environments. Salinity was positively correlated with the potential ammonia oxidation contribution of AOA (p < 0.05), resulting in a potential transition from AOB dominance to AOA dominance in SBBR1 as salinity levels rose. Moreover, autochthonous AOA in PMTW promoted the abundance and ammonia oxidation activities of AOA in SBBR2, further elevating the nitrification removal efficiency after feeding the practical PMTW. AOA demonstrates greater tolerance tothe challenging hypersaline environment, making it a valuable candidate for the treatment of practical industrial wastewater with high salinity and organic content.

The single and combined effects of sulfamethazine and cadmium on soil nitrification and ammonia-oxidizing microorganisms.

The coexistence of antibiotics and heavy metals in soil has attracted increasing attention due to their negative effects on microorganisms. However, how antibiotics and heavy metals affect functional microorganisms related to nitrogen cycle remains unclear. The goals of this work were to explore the individual and combined effects of sulfamethazine (SMT) and cadmium (Cd), selected as target pollutants in soil, on potential nitrification rates (PNR) and ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) structure and diversity by 56-day cultivation experiment. Results showed that PNR in Cd- or SMT-treated soil decreased at the beginning of the experiment and then increased over time. PNR was significantly correlated with AOA and AOB-amoA relative abundance (P < 0.01). SMT addition (10 and 100mgkg-1) significantly improved AOA activity by 13.93% and 17.93%, respectively, and had no effect on AOB at day 1. Conversely, Cd at 10mgkg-1 significantly inhibited AOA and AOB by 34.34% and 37.39%, respectively. Moreover, the relative abundance of AOA and AOB in combined SMT and Cd addition clearly higher relative to single Cd at 1day. The single and combined Cd and SMT increased and reduced the community richness of AOA and AOB, respectively, but reduced the diversity of both after 56days. Cd and SMT treatments significantly changed the relative abundance of AOA phylum levels and AOB genus levels in the soil. It was mainly manifested in reducing the relative abundance of AOA Thaumarchaeota, and increasing the relative abundance of AOB Nitrosospira. Besides, AOB Nitrosospira was more tolerant to the compound addition of both than single application.

Ammonia-oxidizing archaea and comammox Nitrospira clade B as freeze–thaw resistant nitrifiers in wetland soils

Wetland ecosystems are hotspots for nitrogen cycling, while the community dynamics of nitrification-driving microbes include ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia oxidizer (comammox) Nitrospira, and nitrite-oxidizing bacteria were not well-studied. In this study, we investigated the nitrification process in typical inland and coastal wetlands in northern China and found a high diversity of ammonia oxidizers. To simulate the freezing-thawing state under natural environment, the soil samples were first frozen at −20 °C for two months, and then gradually thawed at 4 °C. Further microcosm incubation combined with 13C-DNA-stable isotope probing analyses showed that after the freeze–thaw cycle, only the activities of AOA and comammox Nitrospira clade B recovered. The results indicated that these two groups of nitrifiers were more freeze–thaw resistant, which is in line with literature showing that AOA and comammox Nitrospira clade B were relatively more abundant than their counterparts in low-temperature environments. We tested, for the first time, the cold-shock resilience of nitrifying microbes in wetland soils and spotted candidates driving nitrification under fluctuating temperatures.

Long-acting mechanisms of concentrated urea application — High urea concentrations are biological inhibitors

The concentrated application of urea (CAU; including band and hole placements) promotes cereal crop (e.g., rice and summer maize) yields and nitrogen (N) use efficiency by prolonging the retention of N fertilizer in the soil and reducing N loss. However, the long-acting mechanisms of CAU are not well understood. This study investigated the interactions between N transformation and soil microbes in the special micro-region around the fertilization point with the CAU, using a simulation experiment with two types of soil (silty loam and sandy loam). The soil samples were subjected to six N treatments: 1000, 3000, 5000, 10,000, 30,000 mg N kg−1, and dicyandiamide with 1000 mg N kg−1; no urea treatment was a control. Soil bacterial community compositions (examined using MiSeq sequencing), the abundance of ammonia-oxidizing microbes (quantified using real-time PCR), including ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and the soil chemical properties were assessed at 20 and 60 days after urea application. The high soil ammonium concentration caused by CAU affected the soil bacterial community by changing the soil chemical properties. Soil ammonium concentration and pH were the main factors affecting microbial communities and amoA gene abundance of AOA and AOB. The 10,000 and 30,000 mg N kg−1 dosages for the silty loam soil and 30,000 mg N kg−1 dosage for the sandy loam soil in this simulation experiment significantly (p < 0.05) reduced bacterial α-diversity, amoA gene abundance of AOA and AOB, and inhibited nitrification throughout the culture period. However, the inhibitory effects of high soil N application concentration on nitrification weakened as the culture time increased. Overall, CAU acted as a biological nitrification inhibitor by maintaining high soil ammonium concentration, which decreases activity of AOA and AOB amoaA genes for a long time (>60 days).

The Responses of Ammonia-Oxidizing Microorganisms to Different Environmental Factors Determine Their Elevational Distribution and Assembly Patterns.

The assembly mechanisms shaping the elevational patterns of diversity and community structure in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are not well understood. We investigated the diversities, co-occurrence network patterns, key drivers, and potential activities of AOA and AOB communities along a large altitudinal gradient. The α-diversity of the AOA communities exhibited a monotonically decreasing pattern with increasing elevation, whereas a sinusoidal pattern was observed for the AOB communities. The mean annual temperature was the single factor that most strongly influenced the α-diversity of the AOA communities; however, the interactions of plant richness, soil conductivity, and total nitrogen made comparable contributions to the α-diversity of the AOB communities. Moreover, the β-diversities of the AOA and AOB communities were divided into two distinct clusters by elevation, i.e., low- (1800-2600m) and high-altitude (2800-4100m) sections. These patterns were attributed mainly to the soil pH, followed by variations in plant richness along the altitudinal gradient. In addition, the AOB communities were more important to the soil nitrification potential in the low-altitude section, whereas the AOA communities contributed more to the soil nitrification potential in the high-altitude section. Overall, this study revealed the key factors shaping the elevational patterns of ammonia-oxidizing communities and might predict the consequences of changes in ammonia-oxidizing communities.

Insight into the role of competition in niche differentiation between ammonia-oxidizing archaea and bacteria in ammonium-rich alkaline soil: A network-based study

Interspecific competition between ammonia-oxidizing archaea (AOA) and bacteria (AOB) has been documented, however, its significance in niche differentiation between these nitrifiers under ammonia-rich conditions remains elusive. A network-oriented microcosm incubation study was established to improve our understanding of their interspecific competition. A high ammonium concentration was maintained during the incubation by regularly supplementing urea, and the growth of AOB was retarded to different extents using the AOB inhibitors 1-octyne (OC) and 3,4-dimethylpyrazole phosphate (DMPP) as amendments. In parallel, a 13CO2-stable isotope probing (SIP) incubation study was conducted to investigate the metabolic activity of AOA and AOB under ammonium-rich conditions, with and without DMPP amendment. The results of the network-oriented microcosm incubation indicated that the growth of AOA was highly and negatively correlated with the growth of AOB (r = −0.94, P < 0.001). Network analysis of the whole prokaryotes showed that the majority of AOA phylotypes formed a module independent of AOB phylotypes, indicating their distinct niche preferences. In another distinctive module, we found the remaining AOA to have a coexclusion pattern with AOB, indicating a competitive relationship and a positive connection between AOB and many taxa capable of nitrite/nitrate metabolism, in particular denitrification. The SIP study confirmed that all AOA and AOB phylotypes retained in the network were autotrophically active. It was also shown that the phylotype susceptible to AOB competition was closely related to Nitrososphaera viennensis EN76. Overall, the results demonstrate that both niche preference and interspecific competition contribute to niche partitioning between AOA and AOB. Our results also showed that a tight connection between AOB and other nitrogen-cycling microorganisms may be responsible for substantial nitrogen loss.

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.

Potential nitrification activity reflects ammonia oxidizing bacteria but not archaea activity across a soil-sediment gradient

Terrestrial-marine ecosystems have important ecologically relevant roles influencing the retention and mobility of nitrogen entering coastal ecosystems. The sharp physico-chemical gradients represent an ideal environment to elucidate the relative contributions of ammonia oxidizing archaea (AOA) and bacteria (AOB) to the nitrification process. Here we examined the activity of ammonia oxidisers (AO) across two coastal bays soil-sediment gradients to explore the functional shift from AOA to AOB, and determine if transcriptional activity within the environment (in situ) was emulated in laboratory potential nitrification activity incubations. To do this gene and transcripts abundance and diversity were measured along with potential nitrification activity (PNA) and recovery nitrification potential (RNP) from a series of soil, interface and sediment sites. We compared the composition of amoA transcript community structure in situ vs. PNA/RNP to see if the active AOA and AOB were similar in the environment and in the laboratory experiments. AOA was dominant at gene and transcript level in soil and interphase sites, but active transcripts in situ did not match those within the PNA/RNP assays. AOB was dominant at gene and transcript level in sediments and here transcripts in situ and within the PNA/RNP were similar. A high correlation between AOB transcripts and PNA in sediments was observed but a negative correlation for AOA in soils was seen. Our data indicates that while the PNA/RNP may be a good proxy for AOB activity in these sediments, it was not for AOA dominated soil due to unfavorable incubation conditions.

Effects of short-term soil tillage practice on activity and community structure of ammonia-oxidizing bacteria and archaea under the double-cropping rice field.

The potential nitrification activity (PNA), population size and community composition of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in paddy soil from a short-term (5years) tillage field experiment conducted at tillering stage of late rice were investigated using the shaken slurry method and quantitative real-time polymerase chain reaction. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue returning (NT) and rotary tillage with all crop residues removed as a control (RTO). The results showed that PNA in paddy soil of CT, RT and NT treatments was higher than that of RTO treatment, and the abundance of AOA and AOB was much higher in paddy soil of CT, RT and NT treatments than RTO treatment. Meanwhile, PNA and the abundance of AOB and AOA in paddy soil were greatly enhanced by combined application of tillage and crop residue, whereas PNA and the abundance of AOB and AOA in paddy soil were decreased by combined application of no-tillage and crop residue. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than AOA. The results also showed that PNA and the population sizes of AOB and AOA in crop incorporation treatments were higher than that of crop residue removed treatment. Cluster and redundancy analyses indicated that crop residue effect played a more important role in shaping AOA community structure compared to short-term tillage management. The results indicated that AOB rather than AOA functionally dominated ammonia oxidation in the double-cropping rice paddy soil, the activities of AOB and AOA were increased and the community structure was also changed under the combination of conventional tillage, rotary tillage and crop residue condition. The activity and community structure of AOB and AOA, which were affected by the combination of tillage and crop residue managements, play an important role in cycling of nitrogen.

Immobilization of active ammonia-oxidizing archaea in hydrogel beads

Ammonia-oxidizing archaea (AOA) are major players in the nitrogen cycle but their cultivation represents a major challenge due to their slow growth rate and limited tendency to form biofilms. In this study, AOA was embedded in small (~2.5 mm) and large (~4.7 mm) poly(vinyl alcohol) (PVA)—sodium alginate (SA) hydrogel beads cross-linked with four agents (calcium, barium, light, or sulfate) to compare the differences in activity, the diffusivity of nitrogen species (NH4+, NO2−, and NO3−), and polymer leakage in batch systems over time. Sulfate-bound PVA-SA beads were the most stable, releasing the lowest amount of polymer without shrinking. Diffusion coefficients were found to be 2 to 3 times higher in hydrogels than in granules, with ammonium diffusivity being ca. 35% greater than nitrite and nitrate. Despite a longer lag phase in small beads, embedded AOA sustained a high per volume rate of ammonia oxidation compatible with applications in research and wastewater treatment.

Ammonia-oxidizing bacteria play an important role in nitrification of acidic soils: A meta-analysis

Our knowledge of the abundance and distribution of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) has substantially expanded over the past decade, but their relative contributions to soil nitrification remain debated, particularly at a global scale. Nitrification inhibitor 1-octyne is the only available selective inhibitor that can exclusively inhibit AOB but not AOA activity, making it a powerful tool to differentiate the functional importance of AOB vs AOA in nitrification. Here, we conducted a meta-analysis of laboratory incubation studies with 1-octyne as the nitrification inhibitor to display a panoramic view of the relative contribution of AOB in soil nitrification across various terrestrial ecosystems. The most pronounced reduction of nitrification rates by 1-octyne was found in cropland (71.4%), followed by grassland (59.6%), forestland (53.2%) and wetland (44.0%), indicating a more dominant role of AOB over AOA in upland soils than in wetland soils. The response ratio of soil nitrification rates with 1-octyne addition to that without 1-octyne addition was negatively correlated to soil pH in upland soils, suggesting that a greater proportion of nitrification was inhibited by 1-octyne with higher soil pH. However, the reduction of nitrification rate by 1-octyne was estimated to be 59.5% in acidic soils (pH ≤ 6.5), indicating a major role of AOB in acidic soil nitrification. The proportion of nitrification rate reduced by 1-octyne was greater in soils incubated in slurry and with nitrogen additions than in microcosm and without nitrogen additions, and this should be taken into consideration during the incubation experiments. Altogether, this meta-analysis provides evidence for an equally or more important role of AOB in nitrification from global acidic soils, advancing our understanding of the microbial nitrification process, which is fundamental to the sustainable management of nitrogen in soils.

Soil ammonia-oxidizing archaea in a paddy field with different irrigation and fertilization managements

Because ammonia-oxidizing archaea (AOA) are ubiquitous and highly abundant in almost all terrestrial soils, they play an important role in soil nitrification. However, the changes in the structure and function of AOA communities and their edaphic drivers in paddy soils under different fertilization and irrigation regimes remain unclear. In this study, we investigated AOA abundance, diversity and activity in acid paddy soils by a field experiment. Results indicated that the highest potential ammonia oxidation (PAO) (0.011 μg NO2- –N g-1 d.w.day-1) was found in T2 (optimal irrigation and fertilization)—treated soils, whereas the lowest PAO (0.004 μg NO2- –N g-1 d.w.day-1) in T0 (traditional irrigation)- treated soils. Compared with the T0—treated soil, the T2 treatment significantly (P < 0.05) increased AOA abundances. Furthermore, the abundance of AOA was significantly (P < 0.01) positively correlated with pH, soil organic carbon (SOC), and PAO. Meanwhile, pH and SOC content were significantly (P < 0.05) higher in the T2—treated soil than those in the T1 (traditional irrigation and fertilization)- treated soil. In addition, these two edaphic factors further influenced the AOA community composition. The AOA phylum Crenarchaeota was mainly found in the T2—treated soils. Phylogenetic analysis revealed that most of the identified OTUs of AOA were mainly affiliated with Crenarchaeota. Furthermore, the T2 treatment had higher rice yield than the T0 and T1 treatments. Together, our findings confirm that T2 might ameliorate soil chemical properties, regulate the AOA community structure, increase the AOA abundance, enhance PAO and consequently maintain rice yields in the present study.

Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils.

Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.

Variation, distribution, and diversity of canonical ammonia-oxidizing microorganisms and complete-nitrifying bacteria in highly contaminated ecological restoration regions in the Siding mine area

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (PN) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and PN values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH3 and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the β-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.

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.

Survival strategies of ammonia-oxidizing archaea (AOA) in a full-scale WWTP treating mixed landfill leachate containing copper ions and operating at low-intensity of aeration

Recent studies indicate that ammonia-oxidizing archaea (AOA) may play an important role in nitrogen removal by wastewater treatment plants (WWTPs). However, our knowledge of the mechanisms employed by AOA for growth and survival in full-scale WWTPs is still limited. Here, metagenomic and metatranscriptomic analyses combined with a laboratory cultivation experiment revealed that three active AOAs (WS9, WS192, and WS208) belonging to family Nitrososphaeraceae were active in the deep oxidation ditch (DOD) of a full-scale WWTP treating landfill leachate, which is configured with three continuous aerobic-anoxic (OA) modules with low-intensity aeration (≤ 1.5 mg/L). AOA coexisted with AOB and complete ammonia oxidizers (Comammox), while the ammonia-oxidizing microbial (AOM) community was unexpectedly dominated by the novel AOA strain WS9. The low aeration, long retention time, and relatively high inputs of ammonium and copper might be responsible for the survival of AOA over AOB and Comammox, while the dominance of WS9, specifically may be enhanced by substrate preference and uniquely encoded retention strategies. The urease-negative WS9 is specifically adapted for ammonia acquisition as evidenced by the high expression of an ammonium transporter, whereas two metabolically versatile urease-positive AOA strains (WS192 and WS208) can likely supplement ammonia needs with urea. This study provides important information for the survival and application of the eutrophic Nitrososphaeraceae AOA and advances our understanding of archaea-dominated ammonia oxidation in a full-scale wastewater treatment system.

An RNA-based study of the distribution of ammonia-oxidizing microorganisms in vertical sediment

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play crucial roles in ammonia nitrogen degradation in freshwater lake sediment. However, studies on ammonia-oxidizing microorganisms (AOM) in vertical sediment are still limited, especially with respect to the quantitative analysis of the vertical distribution of active AOM at the RNA level. Herein, by researching the AOM in a 75 cm vertical sediment from Lake Taihu, we found that although the total abundance of AOB throughout the whole vertical sediment surpassed that of AOA, active AOA had a closer correlation with the potential nitrification rate than active AOB. The active transcription abundance of AOM generally decreased with increasing depth, especially for AOA, while that of AOB decreased slightly. Compared to active transcription, the total abundance of AOM varied little. The community structures of AOA and AOB changed significantly with increasing depth, and Group I.1a and Nitrosomonas were the predominant clusters, respectively. Ultimately, our study demonstrated that research methods based on the RNA level can accurately reflect the vertical variation in AOM.

Response of ammonia oxidation activities to water-level fluctuations in riparian zones in a column experiment

Biogeochemical hotspots of nitrogen cycling such as ammonia oxidation commonly occur in riparian ecosystems. However, the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to water-level fluctuations (WLF) in riparian zones remain unclear. In this study, two patterns of WLF (gradual waterlogging and drying) were investigated in a 9-month column experiment, and the abundances and activities of AOA and AOB were investigated. The recovery evaluation revealed AOB abundance had not returned to the initial level at the end of the experiment, while AOA abundance had recovered nearly completely. AOA outnumbered AOB at almost all depths, and AOA showed higher resistance and adaptation to WLF than AOB. However, higher microbial abundance was not always linked to the larger contribution to nitrification. Changes in environmental parameters such as moisture and dissolved oxygen caused by WLF instead of ammonia-oxidizing microorganism (AOM) abundance might play a key role in regulating the expression of amoA gene and thus the activity of ammonia oxidizers. In addition, the community structure of AOM evolved over the incubation period. The composition of AOA species in sediment changed in the same way as that in soil, and the Nitrosopumilus cluster showed strong resistance to WLF. Conversely, waterlogging changed the community structure of AOB in soil while drying had no significant effect on the AOB community structure in sediment. This study suggests that the ammonia oxidizers will respond to WLF and eventually affect N fate in riparian ecosystems considering the coupling with other N transformation processes.

Temperature-dependent changes in active nitrifying communities in response to field fertilization legacy

Using DNA-based stable isotope probing (SIP) in microcosms, we demonstrate the shifts in active nitrifying communities in soil from field plots imposed by 8 years of mineral fertilizer N (NPK) or manure (M) applications compared with an unfertilized control (CK), and associated shifts in their temperature sensitivity. DNA-SIP indicates that ammonia-oxidizing archaea (AOA) were labeled to a much greater extent in the CK soil (74.6%) than in the NPK-amended (19.8%) or M-amended (27.1%) soils at 28 °C. In contrast, NPK soil showed the highest labeling of ammonia-oxidizing bacteria (AOB) (23.3%) relative to M (4.03%) and CK (2.42%) soils. This is further supported by significant decreases in the 13C-amoA gene ratios of AOA/AOB in the NPK (4.14) and M (8.63) compared with CK (46.4) soils at 28 °C, while little difference was observed at 35 °C. The relative abundance of active AOA or AOB in the manure was between that in the CK and NPK soils. This may be attributable to the slower release of ammonium mineralized from manure than from urea. The active AOA in soil microcosms were dominated by Nitrososphaera viennensis-like groups regardless of fertilization history or temperature. Nitrosomonas communis-like AOB may be more adapted to the higher temperature than Nitrosospira cluster 3-like AOB. The labeling of nitrite oxidizers (nitrite-oxidizing bacteria) was lowest in NPK soil and was higher at 28 °C than 35 °C regardless of fertilization treatment. The finding indicates that intensified anthropogenic N inputs in the field may select for distinct active nitrifying communities that exhibited different temperature sensitivities.