Ammonia-oxidizing Archaea Research Articles

Shifts in soil ammonia-oxidizing community maintain the nitrogen stimulation of nitrification across climatic conditions.

Anthropogenic nitrogen (N) loading alters soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundances, likely leading to substantial changes in soil nitrification. However, the factors and mechanisms determining the responses of soil AOA:AOB and nitrification to N loading are still unclear, making it difficult to predict future changes in soil nitrification. Herein, we synthesize68 field studies around the world to evaluate the impacts of N loading on soil ammonia oxidizers and nitrification. Across a wide range of biotic and abiotic factors, climate is the most important driver of the responses of AOA:AOB to N loading. Climate does not directly affect the N-stimulation of nitrification, but does so via climate-related shifts in AOA:AOB. Specifically, climate modulates the responses of AOA:AOB to N loading by affecting soil pH, N-availability and moisture. AOB play a dominant role in affecting nitrification in dry climates, while the impacts from AOA can exceed AOB in humid climates. Together, these results suggest that climate-related shifts in soil ammonia-oxidizing community maintain the N-stimulation of nitrification, highlighting the importance of microbial community composition in mediating the responses of the soil N cycle to N loading.

Stability of ammonia oxidizer communities upon nitrogen fertilizer pulse disturbances is dependent on diversity

Diversity of the soil microbial community is an important factor affecting its stability against disturbance. However, the impact of the decline in soil microbial diversity on the stability of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is not known, particularly considering the repeated soil nutrient disturbances occurring in modern agricultural systems. Here, we conducted a microcosm experiment and modified the soil microbial diversity using the dilution-to-extinction approach to determine the stability and population dynamics of AOB and AOA communities with repeated nitrogen (N) fertilizer application. Our results demonstrated that the AOB community became more abundant and stable against repeated disturbances by N in the treatments with the highest microbial diversity. In contrast, the abundance of AOA decreased following repeated N fertilizer application, regardless of the microbial diversity. Notably, during the initial application phase, AOA displayed a potential for increased abundance in treatments with high soil microbial diversity. These findings highlight that the soil microbial diversity controls the stability of ammonia oxidizers during short-interval repeated N disturbances.

Local climate conditions explain the divergent climate change effects on (de)nitrification across the grassland biome: A meta-analysis

Ecosystem functions, such as soil nitrogen cycling, are being altered by climate change. The responses of soil (de)nitrification to climate change are different and sometimes opposite across global grasslands. However, it remains unclear how the local environmental conditions and the duration and magnitude of climate change experiments influence these responses. We synthesized the results of 49 studies corresponding to 518 observations on the effects of warming, elevated CO2, and elevated precipitation, and unfolded the reasons for the divergent responses in (de)nitrification to these climate change factors. We found that the responses of (de)nitrification are mainly related to annual precipitation and temperature, and less to the duration and magnitude of experimental treatment. In contrast, soil variables such as pH and organic carbon had no significant effects on these responses. Specifically, the effect of warming on the abundance of ammonia-oxidizing archaea (AOA) shifted from negative for mean annual precipitation (MAP) < 600 mm to positive for MAP>700 mm, whereas the effects on denitrification decreased with mean annual temperature (MAT). The effects of elevated CO2 on nitrification, denitrification and soil nitrate all decreased with MAP, with negative effects observed for MAP>700 mm. The effects of elevated P on nitrification and soil ammonium decreased with MAP, with negative effects observed for MAP>300 mm. The results suggested that in dry regions, altered water availability governs climate change effects, while changed nitrogen availability is likely the main determinant in wet regions. This shows how biochemical models should include local climatic conditions when predicting nitrogen dynamics across the grassland biome under future climate change scenarios.

Tree species richness and functional composition drive soil nitrification through ammonia-oxidizing archaea in subtropical forests

Understanding the links between plant diversity and functional microbiota is crucial for unraveling the mechanisms by which plant communities regulate ecosystem functions. However, the underlying mechanism of how tree diversity influences soil nitrification remains elusive in forest ecosystems. Here we investigated the impacts of tree species richness and their functional composition (including functional identity and functional trait diversity) on the dynamics of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and arbuscular mycorrhizal (AM) fungi using a tree diversity experiment established with 32 native tree species in a subtropical forest biome. Our study revealed that tree species richness had a positive concave-down relationship with the abundance of AOA. Furthermore, the community-weighted mean of leaf nitrogen and specific root length were significant positive factors for the abundances of AOA and AOB, respectively. By contrast, functional trait diversity of specific root length was negatively associated with the biomass of AM fungi. Regression analysis showed that the abundance of AOA was positively correlated with soil net nitrification rates, while the biomass of AM fungi was negatively correlated with soil net nitrification rates. The structural equation model showed that the positive effect of leaf nitrogen on nitrification was driven by the increase in AOA. By contrast, the functional trait diversity of specific root length indirectly increased soil nitrification via a negative impact on the biomass of AM fungi. Taken together, our findings demonstrate that both tree species richness and tree functional composition promoted soil nitrification by increasing the AOA abundance, and emphasize the key role of the interplay between tree diversity and functional microbiota in predicting ecosystem functions.

Comparative biotic and abiotic effects on greenhouse gas emissions from agricultural ecosystems: application of straw or biochar?

Farmland has become a significant contributor to greenhouse gas (GHG) emissions, and research has shown that the addition of straw or biochar may be a viable method for mitigating these emissions. However, there is a lack of understanding regarding the comparative biotic and abiotic effects of straw and biochar amendments on GHG emissions. To address this knowledge gap, we conducted a meta-analysis of 100 published papers to quantify the impact of straw and biochar application on GHG emissions. Our findings indicate that straw application significantly increased CO2 and CH4 emissions from agricultural ecosystems by 46.2% and 113.5%, respectively, but did not have a significant effect on N2O emissions. Conversely, biochar amendment significantly reduced CO2, CH4, and N2O emissions by an average of 11.0%, 31.7%, and 22.8%, respectively. We also found that straw and biochar amendments increased soil pH, soil organic carbon (SOC), and C/N ratio, and there were significant differences between them. Moreover, straw application significantly increased the microbial biomass carbon (MBC) content and microbial quotient by 37.1% and 20.1%, respectively, while biochar application increased the MBC content by 25.0% without a significant effect on the microbial quotient. Furthermore, both straw and biochar applications promoted the nitrification process and increased the abundance of ammonia-oxidizing bacteria (AOB) by 50.7% with straw and by 57.5% and 75.1% with biochar for ammonia-oxidizing archaea (AOA) and AOB, respectively. The denitrification process was also stimulated by straw or biochar amendment, resulting in an increase in the abundance of nirK by 22.9% and 16.8%, respectively. Biochar amendment additionally increased the abundance of nosZ by 29.4%, indicating that the main reason for reducing N2O emissions through biochar application is the conversion of NO3--N to N2. Thus, compared to straw application, biochar application is a more effective method for reducing greenhouse gas emissions.

Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China

BackgroundArchaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.ResultsThe relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.ConclusionsOur results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.

Comammox Nitrospira dominates the nitrification in artificial coniferous forest soils of the Qilian Mountains

Complete ammonia oxidizers (Comammox, CMX) are a newly discovered and important component of the nitrogen cycle. While CMX Nitrospira has been detected in various ecosystems, few studies so far have focused on the relative contribution and co-occurrence network of ammonia oxidizing archaea (AOA), bacteria (AOB), and CMX Nitrospira in artificial forest ecosystems (tree plantations). We evaluated the dynamics of composition, co-occurrence patterns and contribution of soil microbial nitrifiers to nitrification in soil of various tree species with different ages in the Qilian Mountains employing the space for time substitution approach, quantitative PCR and high-throughput sequencing technology. Generally, plantation development significantly reduced soil potential nitrification rates. Inhibition experiments and modular analysis showed that AOA played leading roles in nitrification of abandoned farmland and 17-year-old Hippophae rhamnoides, whereas CMX Nitrospira dominated in 36-year-old Picea crassifolia, 36-year-old Picea crassifolia and Larix gmelinii mixed plantation, and 50-year-old Picea crassifolia. The dominant AOA and CMX Nitrospira lineages in all samples were Group I.1b and Clade B, respectively. The assembly of nitrifier community was governed by stochastic processes, in which dispersal limitation made a significant contribution. The nitrifiers coexist in a mutualistic manner, albeit with possible functional redundancy, while the modular analysis revealed the aggregation pattern of the four modules in different artificial forests' soil. The Mantel test showed that modular formation is mainly affected by NH4+ and SOM. These results broaden our current understanding of the relation between CMX Nitrospira and canonical ammonia oxidizers in terrestrial ecosystems, and provide empirical evidence for not only niche differentiation, but also the relative contribution and co-occurrence patterns of nitrifying communities in an artificial forest ecosystem.

Do biodegradable microplastics cause soil inorganic carbon loss in calcareous soils?

The presence of biodegradable microplastics (MPs) has the potential to affect soil pH, and possibly accelerate or inhibit the loss of soil inorganic carbon (SIC) in calcareous soils. However, most researchers have focused on the release of biotic carbon dioxide (CO2) from soils following MP amendments, and few studies have investigated SIC-derived CO2. In this experiment, three typical biodegradable MPs were applied to three calcareous soils amended with 1 % 13C-labeled (99 % atom) carbonate, and the release of CO2 originating from SIC was quantified. The total CO2 emissions, soil pH, and microbial functional genes involved in soil nitrification and denitrification were also detected. Throughout the experiment, the contribution of 13C-labeled carbonate to total CO2 emissions ranged from 0.42 % to 3.31 %. The impact of biodegradable MPs on SIC-derived CO2 varied with incubation period. At the early stage (≤20 days), the amendment of three biodegradable MPs increased the abiotic CO2 in some cases, and the CO2 emissions from 13C-labeled SIC were positively correlated with the total CO2 originating from the decomposition of SOC and MPs. At the late stage (20–70 days), the presence of biodegradable MPs inhibited the release of CO2 from 13C-labeled carbonate in most treatments. Moreover, there were negative relationships of SIC-derived CO2 with soil pH and the amoA gene of ammonia-oxidizing archaea (AOA), but positive correlations of SIC-derived CO2 with amoA of ammonia oxidizing bacteria (AOB) and nirK and nirS genes encoding nitrate reductase in denitrification. Our results indicate that long-term exposure to biodegradable MPs probably regulates the release of H+ in the nitrification process by controlling AOB, and then controlling the dynamics of SIC in calcareous soils.

Nitrite improved nitrification efficiency and enriched ammonia-oxidizing archaea and bacteria in the simultaneous nitrification and denitrification process

Simultaneous nitrification and denitrification (SND) is effective and energy-saving for wastewater treatment. As an inevitable intermediate product in the SND process, nitrite affects the efficiency of ammonia oxidation and the composition of nitrifiers. To investigate the impact of nitrite on ammonia oxidation efficiency, two reactors performing SND were respectively operated without nitrite (R1 as control) and with 20 mg N/L nitrite addition (R2 as experimental). The total nitrogen removal efficiency was 74.5% in R1 while 99.0% in R2. With nitrite addition (i.e., 20 mg N/L), the ammonia removal rate in R2 increased to 4.5 times of that in R1. The ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) contributed to respective around 46.9% and 41.8% ammonia removal in R2 based on the results of experiments with specific inhibitors. The number of respective AOA and AOB ammonia monooxygenase gene (amoA) copies increased by 280 and 30 times due to nitrite addition, according to the qPCR results. The high-throughput sequencing results illustrated the increase of dominant AOB species from 0.40% in R1 to 1.59% in R2 and the phylogenetic tree analysis revealed a close link to Nitrosospira multiformis. These results indicated that the ammonia removal efficiency was improved and AOA/AOB were enriched by nitrite addition. The specific nitrite reductases in AOA and AOB boosted the adaptation of nitrite addition. This study demonstrated the positive impacts of nitrite addition on the ammonia removal efficiency and rate in the SND process.

Nitrification in the water column of Lake Erie: Seasonal patterns, community dynamics, and competition with cyanobacterial harmful algal blooms

Abstract This study reports directly measured nitrification rates in the water column of western Lake Erie, which is affected by annual cyanobacterial harmful algal blooms, and across all three Lake Erie basins. Over three field seasons, 15NH4+ stable isotope tracers were employed to quantify nitrification rates, and relative abundances of ammonia-oxidizing bacteria and ammonia-oxidizing archaea were determined via qPCR. Nitrification rates ranged from undetectable to 1,270 nmol L-1 d-1 and were generally greatest in the western basin near the Maumee River mouth (a major nutrient source). Nitrification rates were highest in early summer, and often lowest during peak cyanobacterial harmful algal blooms months (August and September), before increasing again in October. In the western basin, nitrification was negatively correlated with cyanobacterial biomass. There were no consistent differences in nitrification rates between the three Lake Erie basins. Over the three years in western Lake Erie, ammonia-oxidizing bacteria and ammonia-oxidizing archaea were often present in high and similar abundances, but overall, ammonia-oxidizing bacteria exceeded ammonia-oxidizing archaea, particularly in 2017. No relationships were observed between nitrification rates and ammonia-oxidizing bacteria and ammonia-oxidizing archaea abundances. Thus, despite abundant ammonia-oxidizer DNA, lower nitrification rates during cyanobacterial harmful algal blooms suggest that nitrifiers were poor competitors for regenerated and available NH4+ during these blooms, as also observed in similar systems. Low nitrification rates during cyanobacterial harmful algal blooms could limit system nitrogen removal via denitrification, a natural pathway for its removal and a valuable ecosystem service. Lower denitrification rates allow more bioavailable nitrogen to remain in the system and support biomass and microcystin production; therefore, these results help explain how non-nitrogen-fixing cyanobacterial harmful algal blooms persist, despite low bioavailable nitrogen concentrations during these blooms, and support management efforts to reduce external nitrogen loading to eutrophic systems.

Effect of co-application of straw and various nitrogen fertilizers on N2O emission in acid soil

In order to explore the alteration of N transformation and N2O emissions in acid soil with the co-application of straw and different types of nitrogen (N) fertilizers, an incubation experiment was carried out for 40 days. There are totally five treatments in the study: (a) without straw and N fertilizer (N0), (b) straw alone application (SN0), (c) straw with NH4Cl (SN1), (d) straw with NaNO3 (SN2), and (e) straw with NH4NO3 (SN3). N2O emissions, soil physicochemical properties, and abundance/activity of ammonia-oxidizing archaea (AOA) were measured. The results showed that the combined application of straw and N enhanced N2O emissions, particularly, SN2 and SN3 treatments. Moreover, the soil pH was lower in co-application treatments and the average decreasing rate was 9.69%. Specially, the pH was lowest in the SN1 treatment. The results of correlation analysis indicated a markedly negative relationship between pH and N2O, as well as a negative relationship between pH and net mineralization rate. These findings suggest that pH alteration can affect the N transformation process in soil and thus influence N2O emissions. In addition, the dominant AOA at the genus level in the SN2 treatment was Nitrosopumilus, and Candidatus nitrosocosmicus in the SN3 treatment. The reshaped AOA structure can serve as additional evidence of the changes in the N transformation process. In conclusion, as the return of straw, the cumulation of N2O from arable acid soil depends on the form of N fertilizer. It is also important to consider how N fertilizer is applied to reduce the possibility of N being lost in the soil as gas.

Archaea predominate in the ammonia oxidation process in the sediments of the Yap and Mariana Trenches.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in oxidizing ammonia to nitrite in different marine environments; however, their relative contribution to ammonia oxidation in the deep-sea sediments is still largely unknown. Sediment samples from seamounts and the Challenger Deep along the arc of the Yap Trench and the Mariana Trench were used for the investigation of the geographical distribution of AOA and AOB at the cDNA level, with associated potential nitrification rates (PNRs) being measured. AOA was predominated by Candidatus Nitrosopumilus and Nitrosopumilaceae, while Methylophaga was the major group of AOB. Significantly higher transcript abundance of the AOA amoA gene than that of AOB appeared in all samples, corresponding to the much higher RNRs contributed to AOA. Both the total and AOA PNRs were significantly higher in the deeper layers due to the high sensitivity of AOA to ammonia and oxygen than in AOB. In the surface layers, TN and TOC had significant positive and negative effects on the distribution of the AOA amoA gene transcripts, respectively, while concentration was positively correlated with the AOB amoA gene transcripts. Our study demonstrated that AOA played a more important role than AOB in the ammonia-oxidizing process that occurred in the sediments of the Yap and Mariana Trenches and would expand the understanding of their ecological contribution to the nitrification process and nitrogen flux of trenches.

Abundance, diversity and physiological preferences of comammox Nitrospira in urban groundwater

Complete ammonia oxidizer (comammox Nitrospira), catalyze complete nitrification process in a single organism, are frequently detected in groundwater ecosystem. However, the ecological niches and environmental driving factors of comammox Nitrospira in urban groundwater are largely unknown. Here we investigated the communities of ammonia oxidizers in urban groundwater located in Shanghai city, China. Quantitative analysis demonstrated the dominance of comammox Nitrospira over classical ammonia oxidizers (ammonia-oxidizing archaea and bacteria, AOA and AOB). Phylogenetic analysis showed clades B and A2 comprise the majority of comammox Nitrospira groups. Temperature was one of the most vital factors affecting comammox Nitrospira community. Furthermore, clade A comammox Nitrospira can be enriched by urea substrate, which was in line with the ability of utilizing urea by the pure clade A comammox culture Nitrospira inopinata. In addition, we observed that relatively low temperature (<20 °C) and high copper levels (>0.04 mg L−1) can stimulate the growth of comammox Nitrospira. Overall, this study revealed the presence, diversity and physiological preferences of comammox Nitrospira in urban groundwater nitrification, shedding insights on the ecological roles of comammox Nitrospira in subsurface environment.

Discrepancy in Response of Complete Ammonia Oxidizers and Ammonia-Oxidizing Bacteria and Archaea in the Lhasa River to High-Elevation Conditions

Discrepancy in Response of Complete Ammonia Oxidizers and Ammonia-Oxidizing Bacteria and Archaea in the Lhasa River to High-Elevation Conditions

Microbial community dynamics and metagenomics reveal the potential role of unconventional functional microorganisms in nitrogen and phosphorus removal biofilm system

The conventional functional microorganisms for nitrogen and phosphorus removal, such as Nitrosomonas, Nitrobacter, Nitrospira and Candidatus Accumulibacter, were hotspots in past research. However, the role of diverse unconventional functional microorganisms was neglected. In this study, a biofilm system was developed to explore the potential role of unconventional functional microorganisms in nutrients removal. According to the results of microbial community dynamics and metagenomics, complete ammonia oxidizing (comammox) bacteria was 20 times more abundant than ammonia-oxidizing bacteria (AOB) at day 121 and its abundance of amoA gene was almost the same as AOB. Although Nitrospira dominated the nitrite-oxidizing bacteria (NOB), diverse unconventional nxrB-containing microorganisms, particularly Chloroflexi, also significantly contributed to the nitrite oxidation. Binning analysis showed that Myxococcota-affiliated Haliangium had the necessary genes owns by phosphorus-accumulating organisms (PAO) and was likely to be the primary PAO since its abundance (6.38 %) was much higher than other conventional PAO (0.70 %). Comparing metagenome-assembled genomes of comammox bacteria with AOB and ammonia-oxidizing archaea (AOA), it possessed potential metabolic versatility in hydrogen and phosphorus, which may be the primary reason for the positive effect of the alternating anaerobic and aerobic conditions on the enrichment of comammox bacteria. Collectively, our findings broaden the understanding on the microbial mechanism of nitrogen and phosphorus removal in biofilm system.

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.

Co-immobilization of AOA strains with anammox bacteria in three different synthetic bio-granules maintained under two substrate-level conditions

Hydrogel encapsulation of ammonium oxidizing archaea (AOA) along with anammox bacteria holds potential to enable mainstream partial nitritation (PN)-anammox process attributing to AOA's high affinity to ammonia and oxygen. This study explored the growth of AOA and anammox in hydrogel-based synthetic biogranules by testing two AOA strains, three types of hydrogel beads and two substrate levels, to identify the optimal combination favoring the concomitant growth of AOA and anammox. The AOA Nitrososphaera viennensis (AOA-NV) exhibited higher abundance (10−2.3±0.6 AOA/16S) than the AOA-DW (10−4.7±0.8 AOA/16S) during the entire experimental period. Amongst the three types of hydrogel beads, the PVA-SA-BaCl2 (140 days) and PVA-SA-H3BO3 beads (>180 days) exhibited better long-term structural stability than the PEGDMA-SA-CaCl2 beads. The PVA-SA-H3BO3 beads exhibited the best long-term stability and both the PVA/SA BaCl2 and PVA-SA-H3BO3 beads had comparable ability to retain AOA, anammox and the overall microbial community. Substrate conditions rather than the bead type primarily controlled the microbial community structure. Modest substrate concentrations (1 mM NH4+-N in the feed and 0.8 mg/L dissolved oxygen (DO) in the reactor during aeration phase) followed by low substrate conditions (0.1 mM NH4+-N and 0.2 mg DO/L) both supported the growth of AOA and anammox, while the low substrate condition also suppressed the growth of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB), with AOA /AOB and anammox/NOB ratio of 0.7 and 0.4 at moderate substrate condition and 16.5 and 2.6 at low substrate condition.

Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China.

Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.

Sediment depth-related variations of comammox Nitrospira: Evidence in the Three Gorges Reservoir, China

The recent discovery of comammox Nitrospira as complete ammonia-oxidizing microorganism has fundamentally revolutionized our understanding of nitrogen cycling in sediment environments. However, knowledge regarding their abundance, biodiversity, community structure, and interactions is predominantly limited to the upper layers (0–20 cm). To address this gap, we collected sediment samples along profiles ranging from 0 to 300 cm in depth at three locations within the middle segment of the Three Gorges Reservoir (TGR), China. Quantitative real-time PCR (qPCR) analyses suggested that comammox bacteria were not only ubiquitous in deep sediments but also more abundant than ammonia-oxidizing bacteria (AOB). Ammonia monooxygenases subunit A (amoA) gene amplicon sequencing illuminated that comammox bacteria were more sensitive to sedimental depth compared to AOB and ammonia-oxidizing archaea (AOA), as evidenced by a more significant decline in community diversity and similarity over distance along sediment vertical profiles. Notably, we discovered that the amoA gene abundance, alpha- and beta-diversity of comammox bacteria exerted an essential contribution to potential nitrification rates according to random forest model. Phylogenetic analysis indicted that most comammox bacteria within sediment samples belonged to clade A.2. Intriguingly, the average relative abundance of comammox clade A.2 displayed a noteworthy rise with sediment depth, whereas clade A.1 demonstrated a converse pattern, unveiling distinct ecological niche adaptations of these two clades along the sediment profile. Ecological network analysis further revealed closer interactions between comammox bacteria and canonical ammonia oxidizers in the superficial layer (0–40 cm), with the network structure gradually simplifying from superficial to deep sediment (200–300 cm). Overall, these findings broaden the current recognition of the geographic distribution and niche segregation of comammox bacteria at the fine scale of the sediments ecosystems and provide insights into sediment depth-related variations of their coexistence network patterns in large freshwater reservoirs.

Ammonia-oxidizing archaea bacteria (AOB) and comammox drive the nitrification in alkaline soil under long-term biochar and N fertilizer applications

Ammonia-oxidizing archaea (AOA), bacteria (AOB) and complete ammonia oxidizers (comammox) take an essential part in soil nitrogen (N) cycling. In case of 8 years biochar and N fertilizer application, nevertheless, the comparative contribution of comammox, AOA and AOB to nitrification is unclear. Our long-term field study on alkaline soil (pHwater 8.49) investigated the impact of biochar and N fertilizer on nitrification rate and potential ammonia oxidation in terms of the soil properties, both physical and chemical, together with the abundance and diversity of AOA, AOB and comammox. The findings revealed that biochar and N fertilizer did not affect the amoA abundance of AOA but increased it in AOB and commamox clade A and clade B, but decreased the diversity of AOA and comammox. Nitrogen fertilization significantly declined the diversity of AOB. The AOB abundance was controlled mainly by pH, whereas the AOA, AOB and comammox Chao1 index were governed by soil microbial biomass carbon (MBC). Additionally, biochar increased the soil nitrification rate with or without N fertilizer, but N fertilizer decreased the soil nitrification rate and potential ammonia oxidation (with nitrite oxidation inhibited) under the same biochar application. Biochar and/or N fertilizer increased the corresponding contribution of AOA and comammox to ammonia oxidation by 143–156 % and 33–395 %, respectively, but suppressed the contribution of AOB. Although the abundance of AOA amoA was obviously greater than that of AOB and comammox, the highest contribution to ammonia oxidation was by AOB in soil not fertilized by N and by comammox in the N-fertilized soil. Our findings suggest that changes in soil properties brought about by biochar and N fertilizer addition can influence the diversity of AOA, AOB and comammox, affecting potential ammonia oxidation and the nitrification rate. The AOB and comammox make a bigger contribution to nitrification than AOA in the alkaline soil.