Diversity Of Ammonia-oxidizing Archaea Research Articles

Rice-fish coculture without phosphorus addition improves paddy soil nitrogen availability by shaping ammonia-oxidizing archaea and bacteria in subtropical regions of South China

Rice-fish coculture (RFC), as a traditional agricultural strategy in China, can optimally utilize the scarce resource, especially in subtropical regions where phosphorus (P) deficiency limits agricultural production. However, ammonia-oxidizing archaea (AOA) and bacteria (AOB) are involved in the ammonia oxidation, but it remains uncertain whether their community compositions are related to the RFC combined with and without P addition that improves soil nitrogen (N) use efficiency. Here, a microcosm experiment was conducted to assess the impacts of RFC combined with and without inorganic P (0 and 50 mg P kg−1 as KH2PO4) addition on AOA and AOB community diversities, enzyme activities and N availability. The results showed that RFC significantly increased available N content without P addition compared with P addition. Moreover, RFC significantly increased urease activity and AOA shannon diversity, and reduced NAG activity and AOB shannon diversity without P addition, respectively. Higher diversity of AOA compared with that of AOB causes greater competition for resources and energy within their habitats, thereby resulting in lower network complexity. Our findings indicated that the abundances of AOA and AOB are influenced through the introduction of fish and/or P availability, of which AOB is linked to N availability. Overall, RFC could improve paddy soil N availability without P addition in subtropical region, which provides a scientific reference for promoting the practices that reduce N fertilizer application in RFC.

Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate.

Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.

Novel database for accA gene revealed a vertical variability pattern of autotrophic carbon fixation potential of ammonia oxidizing archaea in a permeable subterranean estuary

The autotrophic carbon fixation pathway of ammonia-oxidizing archaea (AOA) was the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB) cycle, of which the acetyl-CoA carboxylase α-submit (accA) gene is widely recognized as the indicator. To date, there is no reference database or suitable cut-off value for operational taxonomic unit (OTU) clustering to analyze the diversity of AOA based on the accA gene. In this study, a reference database with 489 sequences was constructed, all the accA gene sequences was obtained from the AOA enrichment culture, pure culture and environmental samples. Additionally, the 79% was determined as the cut-off value for OTU clustering by comparing the similarity between the accA gene and the 16S rRNA gene. The developed method was verified by analyzing samples from the subterranean estuary and a vertical variation pattern of autotrophic carbon fixation potential of AOA was revealed. This study provided an effective method to analyze the diversity and autotrophic carbon fixation potential of AOA based on accA gene.

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.

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.

Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil.

Anthropogenic nitrogen inputs lead to a high ammonium (NH4+)/nitrate (NO3-) ratio in the soil, which restricts hyphal spreading of soil fungi. Access of symbiotic fungi to roots is a prerequisite for plant-fungal interactions. Hyphosphere bacteria protect fungi from environmental stress, yet the impact of hyphosphere bacteria on adaptation of host fungi to NH4+-enriched conditions remains unclear. By developing soil microcosm assays, we report that a plant-symbiotic fungus, Phomopsis liquidambaris, harbors specific hyphosphere bacteria that facilitate hyphal spreading and assist in the root colonization in NH4+-enriched soil. Genetic manipulation, 16S rRNA gene analysis and coinoculation assays revealed that the genus Enterobacter was enriched in the hyphosphere of NH4+-sensitive wild-type compared to NH4+-preferring nitrite reductase-deficient strain. The representative Enterobacter sp. SZ2-promoted hyphal spreading is only evident in nonsterilized soil. We further identified an increased abundance and diversity of ammonia-oxidizing archaea (AOA) and a synchronously decreased NH4+:NO3- ratio following SZ2 inoculation. Microbial supplementation and inhibitor assays showed that AOA-mediated reduction in NH4+:NO3- ratio is responsible for SZ2-enhanced fungal adaptation to NH4+-enriched conditions. The Ph. liquidambaris-Enterobacter-AOA triple interaction promoted rice growth in NH4+-enriched soil. Our study reveals the essential role of hyphosphere microorganism-based hyphal spreading in plant-fungal symbiosis establishment within nitrogen-affected agroecosystems.

Dichlorodiphenyltrichloroethane inhibits soil ammonia oxidation by altering ammonia-oxidizing archaeal and bacterial communities

Dichlorodiphenyltrichloroethane (DDT), a persistent organic pollutant, has known effects on natural microbes. However, its effects on soil ammonia-oxidizing microbes, significant contributors to soil ammoxidation, remain unexplored. To address this, we conducted a 30-day microcosm experiment to systematically study the effects of DDT contamination on soil ammonia oxidation and the communities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings revealed that DDT inhibited soil ammonia oxidation in the early stage (0–6 days), but it gradually recovered after 16 days. The copy numbers of amoA gene of AOA decreased in all DDT-treated groups from 2 to 10 days, while that of AOB decreased from 2 to 6 days but increased from 6 to 10 days. DDT influenced the diversity and community composition of AOA but had no significant effect on AOB. Further, the dominant AOA communities comprised uncultured_ammonia-oxidizing_crenarchaeote and Nitrososphaera sp. JG1: while the abundance of the latter significantly and negatively correlated with NH 4+-N (P ≤ 0.001), DDT (0.001 < P ≤ 0.01), and DDD (0.01 < P ≤ 0.05) and positively correlated with NO3−-N (P ≤ 0.001), that of the former significantly and positively correlated with DDT (P ≤ 0.001), DDD (P ≤ 0.001), and NH 4+-N (0.01 < P ≤ 0.05) and negatively correlated with NO3−-N (P ≤ 0.001). Among AOB, the dominant group was the unclassified Nitrosomonadales in Proteobacteria, which showed significant negative correlation with NH 4+-N (0.01 < P ≤ 0.05) and significant positive correlation with NO3−-N (0.001 < P ≤ 0.01). Notably, among AOB, only Nitrosospira sp. III7 exhibited significant negative correlations with DDE (0.001 < P ≤ 0.01), DDT (0.01 < P ≤ 0.05), and DDD (0.01 < P ≤ 0.05). These results indicate that DDT and its metabolites affect soil AOA and AOB, consequently affecting soil ammonia oxidation.

Spatial distribution of ammonia oxidizers in marine sediments of the Bohai, Yellow and East China Seas

Ammonia oxidation, an essential process within the global nitrogen cycle, is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). To date, the current knowledge on the biogeography of AOA and AOB in the ocean across a large geographic distance remains poorly known. In this study, the abundance, microbial composition, and diversity of AOA and AOB in marine sediments collected from the Bohai Sea, Yellow Sea, and East China Sea were characterized by employing quantitative PCR and Illumina Miseq sequencing of both archaeal and bacterial amoA genes. qPCR analysis demonstrated significantly higher abundances of archaeal amoA genes than those of bacterial amoA genes with AOA/AOB ratios varying from 1.59 to 292.88, suggesting a greater contribution of AOA to nitrification in the seas. Nitrosopumilus and Nitrosospira were the predominant clusters of AOA and AOB respectively in all sediment samples. The distribution pattern of both AOA and AOB communities revealed by PCoA (principal coordinate analysis) showed distinct geographic separation of sediment samples from the three seas. Correlation analysis indicated that ammonia (NH4+-N) and nitrate (NO3−-N) content were the main selective forces leading to the distinct biogeography of the two ammonia oxidizers in the ocean. The results are of great significance in improving our understanding of the contribution of AOA and AOB in the nitrogen transformation in the marine ecosystem and providing insights into the environmental factors that shape the assembly of aerobic ammonium oxidizers.

Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.

Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.

Stochastic factors drive dynamics of ammonia-oxidizing archaeal and bacterial communities in aquaculture pond sediment.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play an important role in nitrification, which is essential in the global nitrogen cycle. However, their dynamics and the underlying community processes in agricultural ecosystems under disturbance remain largely unknown. In this study we examined the spatiotemporal dynamics of AOA and AOB communities and analyzed their community processes in the sediment of aquaculture ponds across three different areas in China. We found some significant temporal changes in AOA and AOB community diversity and abundances, but no temporal changes in community composition, despite the significant variations in sediment properties between different sampling times. Nevertheless, significant differences were found for AOA and AOB communities between different areas. Distinct area-specific taxa were detected, and they were found to be important in determining the response of AOA and AOB communities to environmental factors. In addition, geographic distance was found to be significantly correlated with AOA and AOB community composition, which demonstrates that dispersal limitation could significantly contribute to the variations in AOA and AOB communities, and stochastic processes were found to be important in structuring AOA/AOB communities in aquaculture ponds. Taken together, our study indicates that the dynamics of AOA and AOB are based on their community characteristics in aquaculture pond sediment. Our results, for the first time, provide evidence for the dynamics of AOA and AOB communities being driven by stochastic factors in a disturbed environment, and might also be of use in the management of the aquaculture environment.

Substituting Inorganic Fertilizers with Organic Amendment Reduced Nitrous Oxide Emissions by Affecting Nitrifiers’ Microbial Community

Excessive inorganic fertilizers are one of the main causes of nitrous oxide (N2O) emissions. Organic fertilizers can not only reduce the use of nitrogen (N) fertilizers by increasing soil organic matter but are also safe for the environment. The partial replacement of nitrogen (N) fertilizers with organic fertilizers can potentially reduce N2O emissions. To illuminate the best ratio for the nitrogen replacement of inorganic fertilizer, the present experiment was conducted in dryland areas of central Gansu Province and different portions of inorganic N fertilizers (200 kg ha−1); i.e., 0, 50, 37.5, 25, and 12.5% were replaced with commercial organic fertilizers to test their effects on soil physicochemical properties, the grain yield of maize, N2O emissions, and the diversity of ammonia-oxidizing archaea (AOA) and bacterial (AOB) communities. Results showed that the maximum N2O emission was obtained by 100% inorganic fertilizers and the lowest was obtained at the control (no fertilizer). Substituting inorganic fertilizers with organic manure not only reduced N2O emissions but also improved soil organic carbon content and soil moisture and typically improves grain yield and biomass. The highest reduction in N2O emissions was recorded by 50% substitution. Furthermore, 37.5% and 12.5% substitutions did not reduce the grain yield and biomass compared to 100% inorganic fertilizer, and a 37.5% substitution performed better in improving soil fertility. Organic fertilizer increased the amoA copy number of AOA but decreased that of AOB. Nitrososphaera (AOA) and Nitrosospira (AOB) were the most dominant ammonia-oxidizing communities. Structural equation modeling indicated that AOB contributes more N2O emissions than AOA and is more sensitive to changes in pH, moisture, and NO3−−N, and the input of organic fertilizers may affect AOB by influencing soil physicochemical traits. In summary, replacing a reasonable proportion (37.5%) of inorganic fertilizers with organic manure improves soil fertility, reduces N2O emissions, and stabilizes production.

Snow Exclusion Does Not Affect Soil Ammonia-Oxidizing Bacteria and Archaea Communities

Soil ammonia-oxidizing microorganisms play important roles in nitrogen (N) cycling in cold ecosystems, but how changes in snow cover will affect their distribution and associated functional characteristics remains unclear. A snow manipulation experiment was conducted to explore the effects of snow exclusion on soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities and functional characteristics in a spruce forest in the eastern Tibet Plateau. Results showed that the amoA gene abundance and community composition of AOA and AOB did not differ between snow regimes but varied among winter periods. AOA and AOB gene abundances showed a decreasing trend during the snow cover melting period. During the deep snow cover period, Thaumarchaeota and Crenarchaeota in the AOA community decreased significantly, while Proteobacteria and Nitrosospira in the AOB community increased significantly. The main factors affecting the changes in AOA and AOB community diversity and composition were soil MBN, nitrate nitrogen, and temperature, while AOA and AOB community diversity and composition were also significantly correlated with soil enzyme activities related to N cycling. These results recommend that the season-driven variations strongly affected soil ammonia-oxidizing community and functional characteristics more than momentary snow cover change. Such findings offer new insights into how soil N-cycling processes would respond to reduced snowfall in high-altitude regions.

Manure combined with biochar reduces rhizosphere nitrification potential and amoA gene abundance of ammonia-oxidizing microorganisms in acid purple soil

Fertilization and soil environmental factors determine the niche differentiation of ammonia-oxidizing microorganisms, thereby affecting the ammonia-oxidation process. However, the characteristics of rhizosphere potential nitrification rate (PNR), ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) population under manure combined biochar are unclear. In this study, a pot experiment growing lemon was conducted, setting up six treatments, namely no fertilization (CK), chemical fertilizer (CF), manure (M), chemical fertilizer combined with biochar (CFBC), manure combined with biochar (MBC), fresh manure combined with biochar (FMBC). We investigated the effects of manure, chemical fertilizer and manure combined with biochar on soil physical-chemical properties, PNR, and the amoA gene abundance, diversity and structure of AOA and AOB in the rhizosphere. Our results showed that compared with CK treatment, CF and CFBC increases PNR by 19.3–34.7 % in the rhizosphere, M, MBC and FMBC decrease PNR about 60.0 %; CF and CFBC increased AOA amoA gene copies by 40.2–101.7 %, while M, MBC and FMBC treatments decreased it by 66.5–81.9 %, five fertilization treatments decreased the AOB amoA gene copy by 33.1–81.9 %. The redundancy analysis showed that chemical fertilizer and manure combined with biochar affects the population structure of AOA and AOB by pH, available phosphorus (AP), ratio of carbon to nitrogen (C/N), soil moisture content (SMC), nitrate nitrogen (NO3−-N) and ammonium nitrogen (NH4+-N) in the rhizosphere. The results of partial least squares indicated that pH, total nitrogen (TN), AOA amoA gene copy and AOA Shannon index were main factors affecting nitrification potential in the rhizosphere. Therefore, AOA dominates the ammonia oxidation process in the acid purple soil under the condition of chemical fertilizer and pig manure combined with rice husk biochar. Meanwhile, fertilization affected ammonia oxidation process by regulating soil pH and TN in lemon rhizosphere soil.

Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency.

Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.

Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization.

Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha−1 yr−1) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha−1 (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 107 to 1.05 × 107 copies g−1 dry soil, while AOB abundance increased from 3.63 × 107 up to a maximum of 8.24 × 107 copies g−1 dry soil with the N105 treatment (105 kg N ha−1 yr−1). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha−1 yr−1 was optimum for the AOB community and wheat yield in the semi-arid area.

A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China.

The excessive ammonia produced in pond aquaculture processes cannot be ignored. In this review, we present the distribution and diversity of ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing bacteria (AnAOB) in the pond environment. Combined with environmental conditions, we analyze the advantages of AOA and AnAOB in aquaculture water treatment and discuss the current situation of pond water treatment engineering involving these microbes. AOA and AnAOB play an important role in the nitrogen removal process of aquaculture pond water, especially in seasonal low temperatures and anoxic sediment layers. Finally, we prospect the application of bioreactors to purify pond aquaculture water using AOA and AnAOB, in autotrophic nitrogen removal, which can reduce the production of greenhouse gases (such as nitrous oxide) and is conducive to the development of environmentally sustainable pond aquaculture.

Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil

Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha−1 for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.

Soil Amendments Alter Ammonia-Oxidizing Archaea and Bacteria Communities in Rain-Fed Maize Field in Semi-Arid Loess Plateau

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are key drivers of nitrification in rainfed soil ecosystems. However, within a semi-arid region, the influence of different soil amendments on the composition of soil AOA and AOB communities and soil properties of rainfed maize is still unclear. Therefore, in this study, the abundance, diversity, and composition of AOA and AOB communities and the potential nitrification activity (PNA) was investigated across five soil treatments: no fertilization (NA), urea fertilizer (CF), cow manure (SM), corn stalk (MS), and cow manure + urea fertilizer (SC). The AOB amoA gene copy number was influenced significantly by fertilization treatments. The AOB community was dominated by Nitrosospira cluster 3b under the CF and SC treatments, and the AOA community was dominated by Nitrososphaera Group I.1b under the CF and NA amendments; however, manure treatments (SM, MS, and SC) did not exhibit such influence. Network analysis revealed the positive impact of some hub taxonomy on the abundance of ammonia oxidizers. Soil pH, NO3−-N, Module 3, biomass, and AOB abundance were the major variables that influenced the potential nitrification activity (PNA) within structural equation modeling. PNA increased by 142.98–226.5% under the treatments CF, SC, SM, and MS compared to NA. In contrast to AOA, AOB contributed dominantly to PNA. Our study highlights the crucial role of bacterial communities in promoting sustainable agricultural production in calcareous soils in semi-arid loess plateau environments.

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.

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.