Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene

Organic fertilizer significantly mitigates N2O emissions while increase contributed of comammox Nitrospira in paddy soils

Nitrification is the dominant process for nitrous oxide (N2O) production under aerobic conditions, but the relative contribution of the autotrophic nitrifiers (the ammonia-oxidising archaea (AOA), the ammonia-oxidising bacteria (AOB) and the comammox) to this process is still unclear in some soil types. This is particularly the case in paddy soils under different fertilization regimes. We investigated active nitrifiers and their contribution to nitrification and N2O production in a range of unfertilized and fertilized paddy soils, using 13CO2-DNA based stable isotope probing (SIP) technique combined with a series of specific nitrification inhibitors, including acetylene (C2H2), 3, 4-dimethylpyrazole phosphate (DMPP) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). The soils had a long-term history of fertilizer application, including chemical fertilizer only, a mixture of chemical fertilizers (70 %) and chicken manure (30 %) or a mixture of rice straw and chemical fertilizers. 13CO2-DNA-SIP and Illumina MiSeq sequencing demonstrated that comammox clades A.1 and B were active nitrifiers in all fertilized paddy soils. Inhibitor experiment showed that AOB largely contributed to nitrification activity and N2O emission in all paddy soils, while comammox contribution was more significant than AOA. Fertilization considerably altered nitrifiers' relative contribution to nitrification activity and N2O emissions. Applying organic fertilizers significantly decreased the N2O emissions but increased the contribution of comammox to the process. These findings expand the functional ecological niche of comammox, revealing their nitrification role and N2O production in other ecosystems than oligotrophic habitats.

The significant contribution of comammox bacteria to nitrification in a constructed wetland revealed by DNA-based stable isotope probing

The discovery of Comammox bacteria (CMX) has changed our traditional concept towards nitrification, yet its role in constructed wetlands (CWs) remains unclear. This study investigated the contributions of CMX and two canonical ammonia-oxidizing microorganisms, ammonia-oxidizing bacteria (AOB) and archaea to nitrification in four regions (sediment, shoreside, adjacent soil, and water) of a typical CW using DNA-based stable isotope probing. The results revealed that CMX not only widely occurred in sediment and shoreside zones with high abundance (5.08 × 104 and 6.57 × 104 copies g-1 soil, respectively), but also actively participated in ammonia oxidation, achieving ammonia oxidation rates of 1.43 and 2.00 times that of AOB in sediment and shoreside, respectively. Phylogenetic analysis indicated that N. nitrosa was the dominant and active CMX species. These findings uncovered the crucial role of CMX in nitrification of sediment and shoreside, providing a new insight into nitrogen cycle of constructed wetlands.

Nitrite stimulates HONO and NOx but not N2O emissions in Chinese agricultural soils during nitrification

The long-lived greenhouse gas nitrous oxide (N2O) and short-lived reactive nitrogen (Nr) gases such as ammonia (NH3), nitrous acid (HONO), and nitrogen oxides (NOx) are produced and emitted from fertilized soils and play a critical role for climate warming and air quality. However, only few studies have quantified the production and emission potentials for long- and short-lived gaseous nitrogen (N) species simultaneously in agricultural soils. To link the gaseous N species to intermediate N compounds [ammonium (NH4+), hydroxylamine (NH2OH), and nitrite (NO2-)] and estimate their temperature change potential, ex-situ dry-out experiments were conducted with three Chinese agricultural soils. We found that HONO and NOx (NO + NO2) emissions mainly depend on NO2-, while NH3 and N2O emissions are stimulated by NH4+ and NH2OH, respectively. Addition of 3,4-dimethylpyrazole phosphate (DMPP) and acetylene significantly reduced HONO and NOx emissions, while NH3 emissions were significantly enhanced in an alkaline Fluvo-aquic soil. These results suggested that ammonia-oxidizing bacteria (AOB) and complete ammonia-oxidizing bacteria (comammox Nitrospira) dominate HONO and NOx emissions in the alkaline Fluvo-aquic soil, while ammonia-oxidizing archaea (AOA) are dominant in the acidic Mollisol. DMPP effectively mitigated the warming effect in the Fluvo-aquic soil and the Ultisol. In conclusion, our findings highlight NO2- significantly stimulates HONO and NOx emissions from dryland agricultural soils, dominated by nitrification. In addition, subtle differences of soil NH3, N2O, HONO, and NOx emissions indicated different N turnover processes, and should be considered in biogeochemical and atmospheric chemistry models.

Changes in Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria along a Glacier Retreating Chronosequence in the Tianshan Mountains, China

Glaciers retreating due to global warming create important new habitats, particularly suitable for studying ecosystem development where nitrogen is a limiting factor. Nitrogen availability mainly results from microbial decomposition and transformation processes, including nitrification. AOA and AOB perform the first and rate-limiting step of nitrification. Investigating the abundance and diversity of AOA and AOB is essential for understanding early ecosystem development. The dynamics of AOA and AOB community structure along a soil chronosequence in Tianshan No. 1 Glacier foreland were analyzed using qPCR and clone library methods. The results consistently showed low quantities of both AOA and AOB throughout the chronosequence. Initially, the copy numbers of AOB were higher than those of AOA, but they decreased in later stages. The AOB community was dominated by "Nitrosospira cluster ME", while the AOA community was dominated by "the soil and sediment 1". Both communities were potentially connected to supra- and subglacial microbial communities during early stages. Correlation analysis revealed a significant positive correlation between the ratios of AOA and AOB with soil ammonium and total nitrogen levels. These results suggest that variations in abundance and diversity of AOA and AOB along the chronosequences were influenced by ammonium availability during glacier retreat.

Effects of tillage patterns and stover mulching on N2O production, nitrogen cycling genes and microbial dynamics in black soil

Stover-covered no-tillage (NT) is of great significance to the rational utilization of stover resources and improvement of cultivated land quality, and also has a profound impact on ensuring groundwater, food and ecosystem security. However, the effects of tillage patterns and stover mulching on soil nitrogen turnover remain elusive. Based on the long-term conservation tillage field experiment in the mollisol area of Northeast China since 2007, the shotgun metagenomic sequencing of soils and microcosm incubation were combined with physical and chemical analyses, alkyne inhibition analysis to elucidate the regulatory mechanisms of NT and stover mulching on the farmland soil nitrogen emissions and microbial nitrogen cycling genes. Compared with conventional tillage (CT), NT stover mulching significantly reduced the emission of N2O instead of CO2, especially when 33% mulching was adopted, and correspondingly the nitrate nitrogen of NT33 was higher than that of other mulching amounts. The stover mulching was associated with higher total nitrogen, soil organic carbon and pH. The abundance of AOB (ammonia-oxidizing bacteria)-amoA (ammonia monooxygenase subunit A) was substantially increased by stover mulching, while the abundance of denitrification genes was reduced in most cases. Under alkyne inhibition, the tillage mode, treatment time, gas condition and interactions between them noticeably influenced the N2O emission and nitrogen transformation. In CT, NT0 (no mulching) and NT100 (full mulching), the relative contribution of AOB to N2O production was markedly higher than that of ammonia oxidizing archaea. Different tillage modes were associated with distinct microbial community composition, albeit NT100 was closer to CT than to NT0. Compared with CT, the co-occurrence network of microbial communities was more complex in NT0 and NT100. Our findings suggest that maintaining a low-quantity stover mulching could regulate soil nitrogen turnover toward proficiently enhancing soil health and regenerative agriculture, and coping with global climate change.

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

IMPORTANCE

Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.

Role of dry watercourses of an arid watershed in carbon and nitrogen processing along an agricultural impact gradient

In the Mediterranean arid region such as Southeast (SE) Spain, a considerable part of the fluvial network runs permanently dry. Here, many dry watercourses are embedded in catchments where agriculture has brought changes in carbon (C) and nitrogen (N) availability due to native riparian vegetation removal and the establishment of intensive agriculture. Despite their increasing scientific recognition and vulnerability, our knowledge about dry riverbeds biogeochemistry and environmental drivers is still limited, moreover for developing proper management plans at the whole catchment scale. We examined CO₂ and N₂O emissions in five riverbeds in SE Spain of variable agricultural impact under dry and simulated rewetted conditions. Sediment denitrifying capacity upon rewetting was also assessed. We found that, regardless of agricultural impact, all riverbeds can emit CO₂ under dry and wet conditions. Emissions of N₂O were only observed in our study when a long-term rewetting driving saturated sediments was conducted. Besides, most biogeochemical capabilities were enhanced in summer, reflecting the sensitiveness of microbial activity to temperature. Biogeochemical processing variation across rivers appeared to be more controlled by availability of sediment organic C, rather than by agriculturally derived nitrate. We found that the studied dry riverbeds, agriculturally affected or not, may be active sources of CO₂ and contribute to transitory N₂O emissions during rewetting phenomena, potentially through denitrification. We propose that management plans aiming to support ecosystem biogeochemistry through organic C from native vegetation rather than agricultural exudates would help to reduce anthropogenic greenhouse gases emissions and excess of nutrients in the watershed and to control the nitrate inputs to coastal ecosystems.

The contributions of ammonia oxidizing bacteria and archaea to nitrification-dependent N2O emission in alkaline and neutral purple soils

Nitrification is believed to be one of the primary processes of N₂O emission in the agroecological system, which is controlled by soil microbes and mainly regulated by soil pH, oxygen content and NH₄⁺ availability. Previous studies have proved that the relative contributions of ammonia oxidizing bacteria (AOB) and archaea (AOA) to N₂O production were varied with soil pH, however, there is still no consensus on the regulating mechanism of nitrification-derived N₂O production by soil pH. In this study, 1-octyne (a selective inhibitor of AOB) and acetylene (an inhibitor of AOB and AOA) were used in a microcosm incubation experiment to differentiate the relative contribution of AOA and AOB to N₂O emissions in a neutral (pH = 6.75) and an alkaline (pH = 8.35) soils. We found that the amendment of ammonium (NH₄⁺) observably stimulated the production of both AOA and AOB-related N₂O and increased the ammonia monooxygenase (AMO) gene abundances of AOA and AOB in the two test soils. Among which, AOB dominated the process of ammonia oxidation in the alkaline soil, contributing 70.8% of N₂O production derived from nitrification. By contrast, the contribution of AOA and AOB accounted for about one-third of nitrification-related N₂O in acidic soil, respectively. The results indicated that pH was a key factor to change abundance and activity of AOA and AOB, which led to the differentiation of derivation of N₂O production in purple soils. We speculate that both NH₄⁺ content and soil pH mediated specialization of ammonia-oxidizing microorganisms together; and both specialization results and N₂O yield led to the different N₂O emission characteristics in purple soils. These results may help inform the development of N₂O reduction strategies in the future.

Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox)

In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N₂O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.

Soil dissolved organic matters mediate bacterial taxa to enhance nitrification rates under wheat cultivation

Studies have shown that dissolved organic matters (DOMs) may affect soil nutrient availability to plants due to their effect on microbial communities; however, the relationships of soil DOM-bacterial community-N function in response to root exudates remains poorly understand. Here, we evaluated the DOM composition, bacterial taxonomic variation and nitrogen transformation rates in both acidic and alkaline soils, with or without the typical nitrate preference plant (wheat, Triticum aestivum L.). After 30 days' cultivation, DOM compositions such as sugars, amines, amino acids, organic acid, and ketone were significantly increased in soil with wheat vs. bare soil, and these compounds were mainly involved in nitrogen metabolism pathways. Soil core bacterial abundance was changed while bacterial community diversity decreased in response to wheat planting. Function prediction analysis based on FAPROTAX software showed that the bacterial community were significantly (p < 0.05) affiliated with nitrification and organic compound degradation. Additionally, db-RDA and VPA analysis suggested that the contribution of soil DOM to the variance of bacterial community was stronger than that of soil available nutrients. Furthermore, the N-transformation related bacteria like Burkholderiales and ammonia-oxidizing bacteria (AOB) were positively correlated with soil gross nitrification rate, confirming that the soil N transformation was enhanced in both acidic and alkaline soils. Our results provide insight into how soil DOM affects the community structure and function of bacteria to regulate the process of nitrogen transformation in plant-soil system.

Effects of 3,6-dichlorocarbazole on microbial ecology and its degradation in soil

The emerging contaminants polyhalogenated carbazoles (PHCZs) have been verified to be present in soils and sediments globally, and they show dioxin-like toxicity. However, there is a lack of soil ecological risk assessments on PHCZs despite their high detection rate and concentration in soils. The present study investigated the degradation and soil microbial influence of 3,6-dichlorocarbazole (3,6-DCCZ, a frequently detected PHCZ) in soil. The results showed that the half-lives of 3,6-DCCZ at concentrations of 0.100 mg/kg and 1.00 mg/kg were 7.75 d and 16.73 d, respectively. We found that 3,6-DCCZ was transformed into 3-chlorocarbazole (3-CCZ) by dehalogenation in soil. Additionally, intermediate products with higher molecular weights were detected, presumably because the -H on the carbazole ring was replaced by -CH₃, -CH₂-O-CH₃, or -CH₂-O-CH₂CH₃. 3,6-DCCZ exposure slightly increased the soil bacterial abundance and diversity and clearly changed the soil bacterial community structure. Through a comprehensive analysis of FAPROTAX, functional gene qPCR and soil enzyme tests, we concluded that 3,6-DCCZ exposure inhibited nitrification and nitrogen fixation but promoted denitrification, carbon dioxide fixation and hydrocarbon degradation processes in soil. This study provides valuable data for clarifying the PHCZ ecological risk in soil.

Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria

Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.

Revisiting the involvement of ammonia oxidizers and denitrifiers in nitrous oxide emission from cropland soils

Nitrous oxide (N₂O), an ozone-depleting greenhouse gas, is generally produced by soil microbes, particularly NH₃ oxidizers and denitrifiers, and emitted in large quantities after N fertilizer application in croplands. N₂O can be produced via multiple processes, and reduced, with the involvement of more diverse microbes with different physiological constraints than previously thought; therefore, there is a lack of consensus on the production processes and microbes involved under different agricultural practices. In this study, multiple approaches were applied, including N₂O isotopocule analyses, microbial gene transcript measurements, and selective inhibition assays, to revisit the involvement of NH₃ oxidizers and denitrifiers, including the previously-overlooked taxa, in N₂O emission from a cropland, and address the biological and environmental factors controlling the N₂O production processes. Then, we synthesized the results from those approaches and revealed that the overlooked denitrifying bacteria and fungi were more involved in N₂O production than the long-studied ones. We also demonstrated that the N₂O production processes and soil microbes involved were different based on fertilization practices (plowing or surface application) and fertilization types (manure or urea). In particular, we identified the following intensified activities: (1) N₂O production by overlooked denitrifying fungi after manure fertilization onto soil surface; (2) N₂O production by overlooked denitrifying bacteria and N₂O reduction by long-studied N₂O-reducing bacteria after manure fertilization into the plowed layer; and (3) N₂O production by NH₃-oxidizing bacteria and overlooked denitrifying bacteria and fungi when urea fertilization was applied into the plowed layer. We finally propose the conceptual scheme of N flow after fertilization based on distinct physiological constraints among the diverse NH₃ oxidizers and denitrifiers, which will help us understand the environmental context-dependent N₂O emission processes.

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 (P_N) 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 P_N 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.

How nitrification-related N2O is associated with soil ammonia oxidizers in two contrasting soils in China?

As a key process contributing to N₂O emissions, nitrification is regulated by soil microbes and mainly affected by soil pH, NH₃ availability, temperature and O₂ availability. Current knowledge gaps include how nitrification-related N₂O is associated with soil microbes in different pH soils. In the current study, a microcosm incubation experiment was conducted with two contrasting soils of different pH (5.08, 8.30) under controlled conditions. The soils were amended with ammonium sulphate ((NH₄)₂SO₄, 50 mg N kg^-1) combined with or without nitrification inhibitors and incubated under 20 °C, 65% water hold capacity (WHC) for three weeks. N₂O fluxes, mineral nitrogen (N) concentrations and ammonia oxidizers populations were measured during the incubation to investigate the correlations of nitrification-related N₂O with ammonia oxidizers. The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) was used to inhibit nitrification albeit to various inhibition effects with different soils. Acetylene (0.1% v/v C₂H₂), an inhibitor of AOA and AOB ammonia monooxygenase (AMO), was used to distinguish N₂O emissions by nitrifiers and denitrifiers. 1-octyne (5 μM aqueous), a selective specific AOB inhibitor, was used to assess the relative contributions of AOA and AOB to N₂O emissions. The results showed that N₂O yield for AOA and AOB varied with soil pH. AOB was the key microbial player in alkaline soil, contributing about 85% of nitrification-related N₂O. Conversely, about 78% of nitrification-related N₂O was contributed by AOA in acidic soil. Furthermore, there was a significant and positive relationship between mineral N (NO₂^-, NO₃^-), AOA and AOB populations and nitrification-related N₂O in alkaline soil. However, in acidic soil, NO₃^- concentration and AOA had significantly positive relationships with nitrification-related N₂O. To conclude, soil pH was a key factor affecting the contribution of ammonia oxidizers to nitrification-related N₂O emissions. AOA-related N₂O production dominated at low pH (5.08), while AOB-related N₂O was favored in alkaline soil (pH 8.3).

Microcystis blooms aggravate the diurnal alternation of nitrification and nitrate reduction in the water column in Lake Taihu

To explore the effects of Microcystis blooms on nitrogen (N) cycling in the water column, the community structures of the Microcystis-attached and free-living bacteria in Lake Taihu were assessed and a mesocosm experiment was further conducted on the shore of Lake Taihu. The bacterial communities of Microcystis-attached and free-living bacteria were dominated by heterotrophic bacteria, such as Pseudomonas and Massilia, while the relative abundances of the genera related to traditional autotrophic nitrification were surprisingly low. However, the dramatic increase in nitrate (NO₃^-) levels at the daytime suggested that in the mesocosms nitrification did occur, during which the heterotrophic nitrifiers played a predominant role as revealed by the acetylene inhibition experiment. The ammonium (NH₄⁺) concentrations were always maintained at a low level, indicating that most of the substrates for daytime nitrification originated from organic N. The total N being removed during the experiment was much less than the sum of daily NO₃^- reduction, while the decrease in NO₃^- concentration was much higher than the increase in NH₄⁺ concentration during the night, indicating that assimilation was the main explanation for nocturnal NO₃^- reduction. Thus, the cycling of organic N (remineralization) - heterotrophic nitrification - NO₃^- assimilation (reduction) promoted by Microcystis blooms aggravates the diurnal variation of NO₃^- in the water column.

Straw mulching and nitrogen application altered ammonia oxidizers communities and improved soil quality in the alkaline purple soil of southwest China

Microbe-mediated ammonia oxidation is a key process in soil nitrogen cycle. However, the effect of maize straw mulching on the ammonia oxidizers in the alkaline purple soil remains largely unknown. A three-year positioning experiment was designed as follows: straw mulching measures as the main-plot treatment and three kinds of nitrogen application as the sub-plot treatment. We found the contents of soil organic carbon (SOC), total nitrogen (TN), available potassium (AK), available nitrogen (AN), available phosphorus (AP), and NH₄⁺-N were increased after straw mulching and nitrogen application in alkaline purple soil, so did the amoA genes abundance of ammonia-oxidizing archaeal (AOA) and bacterial (AOB). Terminal restriction fragment length polymorphism (T-RFLP) analysis revealed that Thaumarchaeote (448-bp T-RF) was dominated the AOA communities, whereas Nitrosospira sp (111-bp T-RF) dominated the AOB communities. The community compositions of both AOA and AOB were altered by straw mulching and nitrogen application in alkaline purple soil, however, the AOB communities was more responsive than AOA communities to the straw mulching and nitrogen application. Further analysis indicated that SOC and AP were the main factors affecting the abundance and community compositions of AOA and AOB in alkaline purple soil. The present study reported that straw mulching and nitrogen strategies differently shape the soil ammonia oxidizers community structure and abundance, which should be considered when evaluating agricultural management strategies regarding their sustainability and soil quality.

Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications

Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤ 10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

Development of droplet digital PCR assays to quantify genes involved in nitrification and denitrification, comparison with quantitative real-time PCR and validation of assays in vineyard soil

Quantifying genes in soil is important to relate the abundance of soil bacteria to biogeochemical cycles. Quantitative real-time PCR is widely used for quantification, but its use with environmental samples is limited by poor reaction efficiencies or by PCR inhibition through co-purified soil substances. Droplet digital PCR (ddPCR) is a technology for absolute, sensitive quantification of genes. This study optimized eight ddPCR assays to quantify total bacteria and archaea as well as the nitrification (bacterial and archaeal amoA) and denitrification (nirS, nirK, nosZI, nosZII) genes involved in the generation or reduction of the greenhouse gas nitrous oxide. Detection and quantification thresholds were compared with those of quantitative real-time PCR and were equal to, or improved, in ddPCR. To validate the assays using environmental samples, soil DNA was isolated from two vineyards in the Okanagan valley in British Columbia, Canada, over the 2017 growing season. Soil properties related to the observed gene abundances were determined. Total bacteria, nirK, and nosZII increased with time and the soil C/N ratio and NH₄⁺-N concentration affected total archaea and archaeal amoA negatively. The results, compared with those of other studies, showed that ddPCR is a valid alternative to qPCR to quantify genes involved in nitrification or denitrification.

Differential Ecosystem Function Stability of Ammonia-Oxidizing Archaea and Bacteria following Short-Term Environmental Perturbation

Rapidly expanding conversion of tropical forests to oil palm plantations in Southeast Asia leads to soil acidification following intensive nitrogen fertilization. Changes in soil pH are predicted to have an impact on archaeal ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete (comammox) ammonia oxidizers and, consequently, on nitrification. It is therefore critical to determine whether the predicted effects of pH on ammonia oxidizers and nitrification activity apply in tropical soils subjected to various degrees of anthropogenic activity. This was investigated by experimental manipulation of pH in soil microcosms from a land-use gradient (forest, riparian, and oil palm soils). The nitrification rate was greater in forest soils with native neutral pH than in converted acidic oil palm soils. Ammonia oxidizer activity decreased following acidification of the forest soils but increased after liming of the oil palm soils, leading to a trend of a reversed net nitrification rate after pH modification. AOA and AOB nitrification activity was dependent on pH, but AOB were more sensitive to pH modification than AOA, which demonstrates a greater stability of AOA than AOB under conditions of short-term perturbation. In addition, these results predict AOB to be a good bioindicator of nitrification response following pH perturbation during land-use conversion. AOB and/or comammox species were active in all soils along the land-use gradient, even, unexpectedly, under acidic conditions, suggesting their adaptation to native acidic or acidified soils. The present study therefore provided evidence for limited stability of soil ammonia oxidizer activity following intensive anthropogenic activities, which likely aggravates the vulnerability of nitrogen cycle processes to environmental disturbance.IMPORTANCE Physiological and ecological studies have provided evidence for pH-driven niche specialization of ammonia oxidizers in terrestrial ecosystems. However, the functional stability of ammonia oxidizers following pH change has not been investigated, despite its importance in understanding the maintenance of ecosystem processes following environmental perturbation. This is particularly true after anthropogenic perturbation, such as the conversion of tropical forest to oil palm plantations. This study demonstrated a great impact of land-use conversion on nitrification, which is linked to changes in soil pH due to common agricultural practices (intensive fertilization). In addition, the different communities of ammonia oxidizers were differently affected by short-term pH perturbations, with implications for future land-use conversions but also for increased knowledge of associated global nitrous oxide emissions and current climate change concerns.

Thaumarchaea Genome Sequences from a High Arctic Active Layer

The role of archaeal ammonia oxidizers often exceeds that of bacterial ammonia oxidizers in marine and terrestrial environments but has been understudied in permafrost, where thawing has the potential to release ammonia. Here, three thaumarchaea genomes were assembled and annotated from metagenomic data sets from carbon-poor Canadian High Arctic active-layer cryosols.

The role of archaeal ammonia oxidizers often exceeds that of bacterial ammonia oxidizers in marine and terrestrial environments but has been understudied in permafrost, where thawing has the potential to release ammonia. Here, three thaumarchaea genomes were assembled and annotated from metagenomic data sets from carbon-poor Canadian High Arctic active-layer cryosols.

Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils

The effects of temperature on microorganisms in high latitude regions, and their possible feedbacks in response to change, are unclear. Here, we assess microbial functionality and composition in response to a substantial temperature change. Total soil biomass, amoA gene sequencing, extracellular activity assays and soil physicochemistry were measured to assess a warming scenario. Soil warming to 15°C for 30 days triggered a significant decrease in microbial biomass compared to baseline soils (0°C; P &lt; 0.05) after incubations had induced an initial increase. These changes coincided with increases in extracellular enzymatic activity for peptide hydrolysis and phenolic oxidation at higher temperatures, but not for the degradation of carbon substrates. Shifts in ammonia-oxidising bacteria (AOB) community composition related most significantly to changes in soil carbon content (P &lt; 0.05), which gradually increased in microcosms exposed to a persistently elevated temperature relative to baseline incubations, while temperature did not influence AOBs. The concentration of soil ammonium (NH4+) decreased significantly at higher temperatures subsequent to an initial increase, possibly due to higher conversion rates of NH4+ to nitrate by nitrifying bacteria. We show that higher soil temperatures may reduce viable microbial biomass in cold environments but stimulate their activity over a short period.

Aged biochar stimulated ammonia-oxidizing archaea and bacteria-derived N2O and NO production in an acidic vegetable soil

Both nitrous oxide (N₂O) and nitric oxide (NO) emissions are typically high in greenhouse-based high N input vegetable soils. Biochar amendment has been widely recommended for mitigating soil N₂O emissions in agriculture. However, knowledge of the regulatory mechanisms of fresh and aged biochar for both N₂O and NO production during ammonia oxidation is lacking. Two vegetable soils with different pH values were used in aerobic incubation experiments with 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), 1-octyne and acetylene. The relative importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to N₂O and NO production was investigated as influenced by fresh and aged biochar amendments. The results showed that AOA dominated N₂O production in acidic soil, while AOB dominated N₂O production in alkaline soil. Aged biochar stimulated both AOA- and AOB-derived N₂O and NO production by 84.8 and 340%, respectively, in acidic soil but only increased AOA-derived N₂O and NO production in alkaline soil. Fresh biochar amendment increased AOA- and AOB-derived NO in acidic soil and AOA-derived NO in alkaline soil but had negligible effects on AOA- and AOB-derived N₂O in both soils. Fresh biochar decreased AOA-amoA but increased AOB-amoA gene abundances in acidic soil, whereas aged biochar increased AOA- and AOB-amoA gene abundances in both soils. These findings improved our understanding of N₂O and NO production mechanisms under different biochar amendments in alkaline and acidic vegetable soils.

Responses of Active Ammonia Oxidizers and Nitrification Activity in Eutrophic Lake Sediments to Nitrogen and Temperature

Ammonium concentrations and temperature drive the activities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), but their effects on these microbes in eutrophic freshwater sediments are unclear. In this study, surface sediments collected from areas of Taihu Lake (China) with different degrees of eutrophication were incubated under three levels of nitrogen input and temperature, and the autotrophic growth of ammonia oxidizers was assessed using ¹³C-labeled DNA-based stable-isotope probing (SIP), while communities were characterized using MiSeq sequencing and phylogenetic analysis of 16S rRNA genes. Nitrification rates in sediment microcosms were positively correlated with nitrogen inputs, but there was no marked association with temperature. Incubation of SIP microcosms indicated that AOA and AOB amoA genes were labeled by ¹³C at 20°C and 30°C in the slightly eutrophic sediment, and AOB amoA genes were labeled to a much greater extent than AOA amoA genes in the moderately eutrophic sediment after 56 days. Phylogenetic analysis of ¹³C-labeled 16S rRNA genes revealed that the active AOA were mainly affiliated with the Nitrosopumilus cluster, with the Nitrososphaera cluster dominating in the slightly eutrophic sediment at 30°C with low ammonium input (1 mM). Active AOB communities were more sensitive to nitrogen input and temperature than were AOA communities, and they were exclusively dominated by the Nitrosomonas cluster, which tended to be associated with Nitrosomonadaceae-like lineages. Nitrosomonas sp. strain Is79A3 tended to dominate the moderately eutrophic sediment at 10°C with greater ammonium input (2.86 mM). The relative abundance responses of the major active communities to nitrogen input and temperature gradients varied, indicating niche differentiation and differences in the physiological metabolism of ammonia oxidizers that are yet to be described.IMPORTANCE Both archaea and bacteria contribute to ammonia oxidation, which plays a central role in the global cycling of nitrogen and is important for reducing eutrophication in freshwater environments. The abundance and activities of ammonia-oxidizing archaea and bacteria in eutrophic limnic sediments vary with different ammonium concentrations or with seasonal shifts, and how the two factors affect nitrification activity, microbial roles, and active groups in different eutrophic sediments is unclear. The significance of our research is in identifying the archaeal and bacterial responses to anthropogenic activity and climate change, which will greatly enhance our understanding of the physiological metabolic differences of ammonia oxidizers.

Effect of Straw and Straw Biochar on the Community Structure and Diversity of Ammonia-oxidizing Bacteria and Archaea in Rice-wheat Rotation Ecosystems

Ammonia oxidation is the first and rate-limiting step of nitrification, driven by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Straw and straw biochar retention are the popular ways to utilize the agricultural by-products in China, but their long-term effects on AOB and AOA still remain poorly understood. Based on a 7-year plot experiment, which had 4 fertilization regimes: no fertilizer (CK), regular fertilization (RT), straw retention (SR) and straw biochar retention (SB), the abundance and the composition of AOB and AOA was investigated before both the harvest of rice and wheat season by quantitative PCR and 454 high-throughput pyrosequencing, respectively. (1) Compared to RT, straw and straw biochar increased AOB abundance and diversity significantly only in wheat season (P < 0.05), and they both ranked as SB > SR > RT. Among fertilized treatments, a significant difference between SR and RT was found in AOB community composition of the winter season (R value = 0.58, P value = 0.02); (2) In contrast, AOA was almost not responsive to organic addition, except the significant enhancement of abundance by biochar in wheat season; (3) After straw and straw biochar addition, soil potential nitrification rates (PNR) was positive correlated to AOB abundance in both rice and wheat season (P < 0.01), not to AOA abundance (P = 0.211 and 0.068, respectively). This study provides scientific support for the potential of straw utilization to improve nitrification in rice-wheat rotation system with respect to soil ammonia oxidation microorganism.

Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review

While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH₄-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.

Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China

Nitrification driven by ammonia oxidizers is a key step of nitrogen removal in estuarine environments. Spatial distribution characteristics of ammonia-oxidizers have been well understood in mudflats, but less studied in the agricultural soils next to mudflats, which also play an important role in nitrogen cycling of the estuarine ecosystem. In the present research, we investigated ammonia oxidizers' distributions along the Yangtze River estuary in Jiangsu Province, China, sampling soils right next to the estuary (mudflats) and the agricultural soils 100 m away. We determined the relationship between the abundance of amoA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and the potential nitrification rates of the mudflats and agricultural soils. We also identified the environmental variables that correlated with the composition of the ammonia oxidizers' communities by 16S rRNA gene pyrosequencing. Results indicated that agricultural soils have significantly higher potential nitrification rates as well as the AOA abundance, and resulted in strong phylogenetic clustering only in AOA communities. The ammonia oxidizers' community compositions differed dramatically among the mudflat and agricultural sites, and stochasticity played a dominant role. The AOA communities were dominated by the Group 1.1a cluster at the mudflat, whereas the 54D9 and 29i4 clusters were dominant in agriculture soils. The dominant AOB communities in the mudflat were closely related to the Nitrosospira lineage, whereas the agricultural soils were dominated by the Nitrosomonas lineage. Soil organic matter and salinity were correlated with the ammonia oxidizers' community compositions.

Approaches to understanding the ecology and evolution of understudied terrestrial archaeal ammonia-oxidisers

Ammonia-oxidising archaea (AOA) form a phylogenetic group within the phylum Thaumarchaeota and are of ecological significance due to their role in nitrification, an important biogeochemical process. Previous research has provided information on their ecosystem role and potential physiological characteristics, for example, through analyses of their environmental distribution, ecological adaptation and evolutionary history. However, most AOA diversity, assessed using several environmental marker genes, is not represented in laboratory cultures, with consequent gaps in knowledge of their physiology and evolution. The present study critically reviews existing and developing approaches for the assessment of AOA function and diversity and their potential to provide a deeper understanding of these ecologically important, but understudied microorganisms.

Drying and Rainfall Shape the Structure and Functioning of Nitrifying Microbial Communities in Riverbed Sediments

Non-flow periods in fluvial ecosystems are a global phenomenon. Streambed drying and rewetting by sporadic rainfalls could drive considerable changes in the microbial communities that govern stream nitrogen (N) availability at different temporal and spatial scales. We performed a microcosm-based experiment to investigate how dry period duration (DPD) (0, 3, 6, and 9 weeks) and magnitude of sporadic rewetting by rainfall (0, 4, and 21 mm applied at end of dry period) affected stocks of N in riverbed sediments, ammonia-oxidizing bacteria (AOB) and archaea (AOA) and rates of ammonia oxidation (AO), and emissions of nitrous oxide (N2O) to the atmosphere. While ammonium (NH4 +) pool size decreased, nitrate (NO3 -) pool size increased in sediments with progressive drying. Concomitantly, the relative and absolute abundance of AOB and, especially, AOA (assessed by 16S rRNA gene sequencing and quantitative PCR of ammonia monooxygenase genes) increased, despite an apparent decrease of AO rates with drying. An increase of N2O emissions occurred at early drying before substantially dropping until the end of the experiment. Strong rainfall of 21 mm increased AO rates and NH4 + in sediments, whereas modest rainfall of 4 mm triggered a notable increase of N2O fluxes. Interestingly, such responses were detected only after 6 and 9 weeks of drying. Our results demonstrate that progressive drying drives considerable changes in in-stream N cycling and the associated nitrifying microbial communities, and that sporadic rainfall can modulate these effects. Our findings are particularly relevant for N processing and transport in rivers with alternating dry and wet phases - a hydrological scenario expected to become more important in the future.

Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance

Understanding how microorganisms respond to environmental disturbance is one of the key focuses in microbial ecology. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are responsible for ammonia oxidation which is a crucial step in the nitrogen cycle. Although the physiology, distribution, and activity of AOA and AOB in soil have been extensively investigated, their recovery from a natural disturbance remains largely unknown. To assess the recovery capacities, including resistance and resilience, of AOA and AOB, soil samples were taken from a reservoir riparian zone which experienced periodically water flooding. The samples were classified into three groups (flooding, recovery, and control) for a high-throughput sequencing and quantitative PCR analysis. We used a relative quantitative index of both the resistance (RS) and resilience (RL) to assess the variation of gene abundance, alpha-diversity, and community composition. The AOA generally demonstrated a better recovery capability after the flooding disturbance compared to AOB. In particular, AOA were more resilient after the flooding disturbance. Taxa within the AOA and AOB showed different RS and RL values, with the most abundant taxa showing in general the highest RS indices. Soil NH₄⁺ and Fe²⁺/Fe³⁺ were the main variables controlling the key taxa of AOA and AOB and probably influenced the resistance and resilience properties of AOA and AOB communities. The distinct mechanisms of AOA and AOB in maintaining community stability against the flooding disturbance might be linked to the different life-history strategies: the AOA community was more likely to represent r-strategists in contrast to the AOB community following a K-life strategy. Our results indicated that the AOA may play a vital role in ammonia oxidation in a fluctuating habitat and contribute to the stability of riparian ecosystem.

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

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

Ammonia oxidizers and nitrite-oxidizing bacteria respond differently to long-term manure application in four paddy soils of south of China

Nitrification plays an important role in the soil nitrogen (N) cycle, and fertilizer application may influence soil nitrifiers' abundance and composition. However, the effect of long-term manure application in paddy soils on nitrifying populations is poorly understood. We chose four long-term manure experimental fields in the south of China to study how the abundance and community structure of nitrifiers would change in response to long-term manure application using quantitative PCR and Miseq sequencing analyses. Our results showed that manure application significantly increased ammonia oxidizing archaea (AOA) abundance at the ChangSha (CS) and NanChang (NC) sites, while the abundance of ammonia oxidizing bacteria (AOB) represented 4.8- and 12.8- fold increases at the JiaXing (JX) and YingTan (YT) sites, respectively. Miseq sequencing of 16S rRNA genes indicated that manure application altered the community structure of nitrifying populations, especially at the NC and YT sites. The application of manure significantly changed AOA and nitrite oxidizing bacteria (NOB) community structures but not those of AOB, suggesting that AOA and NOB may be more sensitive to manures. Variation partitioning analysis (VPA) and redundancy analysis (RDA) indicated that soil pH, TN, NO₃^--N and water content were the main factors in shaping nitrifying communities. These findings suggest that nitrifiers respond diversely to manure application, and soil physiochemical properties play an important role in determining nitrifiers' abundance and communities with long-term manure addition.

Dominant role of ammonia-oxidizing bacteria in nitrification due to ammonia accumulation in sediments of Danjiangkou reservoir, China

Surface sediments are the inner source of contaminations in aquatic systems and usually maintain aerobic conditions. As the key participators of nitrification process, little is known about the activities and contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. In this study, we determined the net and potential nitrification rates and used 1-octyne as an AOB specific inhibitor to detect the contributions of AOA and AOB to nitrification in surface sediments of Danjiangkou reservoir, which is the water source area of the middle route of South-to-North Water Diversion Project in China. Quantitative PCR and Illumina high-throughput sequencing were used to evaluate the abundance and diversity of the amoA gene. The net and potential nitrification rates ranged from 0.42 to 1.93 and 2.06 to 8.79 mg N kg^-1 dry sediments d^-1, respectively. AOB dominated in both net and potential nitrification, whose contribution accounted for 52.7-78.6% and 59.9-88.1%, respectively. The cell-specific ammonia oxidation rate calculation also revealed the cell-specific rates of AOB were higher than that of AOA. The Spearman's rank correlation analysis suggested that ammonia accumulation led to the AOB predominant role in net nitrification activity, and AOB abundance played the key role in potential nitrification activity. Furthermore, phylogenetic analysis suggested AOB were predominantly characterized by the Nitrosospira cluster, while AOA by the Nitrososphaera and Nitrososphaera sister clusters. This study will help us to better understand the contributions and characteristics of AOA and AOB in aquatic sediments and provide improved strategies for nitrogen control in large reservoirs.

The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions

High and low rates of ammonium supply are believed to favour ammonia-oxidising bacteria (AOB) and archaea (AOA), respectively. Although their contrasting affinities for ammonium are suggested to account for these differences, the influence of ammonia concentration on AOA and AOB has not been tested under environmental conditions. In addition, while both AOB and AOA contribute to nitrous oxide (N₂O) emissions from soil, N₂O yields (N₂O-N produced per NO₂^--N generated from ammonia oxidation) of AOA are lower, suggesting lower emissions when AOA dominate ammonia oxidation. This study tested the hypothesis that ammonium supplied continuously at low rates is preferentially oxidised by AOA, with lower N₂O yield than expected for AOB-dominated processes. Soil microcosms were supplied with water, urea or a slow release, urea-based fertiliser and 1-octyne (inhibiting only AOB) was applied to distinguish AOA and AOB activity and associated N₂O production. Low ammonium supply, from mineralisation of organic matter, or of the fertiliser, led to growth, ammonia oxidation and N₂O production by AOA only, with low N₂O yield. High ammonium supply, from free urea within the fertiliser or after urea addition, led to growth of both groups, but AOB-dominated ammonia oxidation was associated with twofold greater N₂O yield than that dominated by AOA. This study therefore demonstrates growth of both AOA and AOB at high ammonium concentration, confirms AOA dominance during low ammonium supply and suggests that slow release or organic fertilisers potentially mitigate N₂O emissions through differences in niche specialisation and N₂O production mechanisms in AOA and AOB.

Seasonal variation and ex-situ nitrification activity of ammonia oxidizing archaea in biofilm based wastewater treatment processes

The abundance of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) was investigated in full-scale two-stage trickling filters (TF) and moving bed bioreactor (MBBR) treating municipal wastewater. Biofilm samples were collected for 17months from nitrifying TF (NTF), biochemical oxygen demand TF (BTF), and MBBR media. The abundance of AOA and AOB was determined using a quantitative PCR approach targeting the ammonia monooxygenase subunit A gene of archaea and bacteria. AOA were dominant in the NTF and MBBR, while AOB dominated in the BTF. AOA and AOB were more abundant during warmer months, and AOA were detected in the BTF only during warmer months. In laboratory nitrification activity experiments, ammonia oxidation to nitrite decreased when AOA populations from the NTF and MBBR were inhibited, demonstrating that AOA contributed to nitrification. This study has shown that AOA outnumber AOB and contribute to ammonia oxidation in full-scale nitrifying biofilm processes.

Contributions of nitrification and denitrification to N2O emissions from aged refuse bioreactor at different feeding loads of ammonia substrates

Nitrous oxide (N₂O) is a strong greenhouse gas, and its emissions from microbial nitrification (NF) and denitrification (DNF) are a threat to the environment. In the present study, a combined approach consisting of ¹⁵N stable isotope and molecular biology (qPCR) was used to determine the contributions of autotrophic nitrification (ANF), heterotrophic nitrification (HNF), and DNF to N₂O emissions in laboratory incubations of aged refuse for different ammonia (NH₄⁺-N) loads (200, 400, and 800mg·NH₄⁺-N/kg·aged refuse) and incubation times (2-144h). Experimental results showed that the N₂O emissions increased with the increase in applied amount of NH₄⁺-N substrates. Simultaneous nitrification and denitrification (SND) were demonstrated to be present in the incubations of aged refuse. The results of ¹⁵N stable isotope labelling experiment indicated that NF (54.60%-68.8%) and DNF (83.38%-85.90%) contributed to majority of N₂O emissions in the incubations of 24h and 72h, respectively. The results of functional genes (amoA and nosZ) quantification experiments indicated that the high gene copies of amoA and nosZ were present at 24h and 72h, respectively. The study also demonstrated the utility of a combined stable isotope and molecular biology approach. The approaches not only provide similar inferences about the N₂O emissions, but also enable the determination of relative contributions of ANF, HNF, and DNF to N₂O emissions. The results of the study are important in providing guidance to artificially optimize the operating conditions for alleviating N₂O emissions in aged refuse bioreactors.

Ammonia Oxidizers in a Grazing Land with a History of Poultry Litter Application

Poultry litter (PL) is widely applied on grazing lands in Georgia. However, it is not clear how its long-term use affects soil microorganisms and their function. We examined changes in activity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a grazing land with a history of PL application and compared it to treatment with urea ammonium nitrate (UAN). Soil samples (0-15 cm) were collected in 2009 (after 15 yr of PL application) and in 2013 (after 2 yr of no application). The abundance and community composition of ammonia oxidizers (AO) were determined with molecular techniques that targeted Nitrification potential (NP) was used for measuring their activity. Abundance of AO was significantly higher in PL (7.41 and 7.10 log copies g soil for AOB and AOA, respectively) than in UAN plots (6.82 and 6.50 log copies g soil for AOB and AOA, respectively) in 2009. This is consistent with NP, which was higher in PL (0.78 mg NO -N kg h) than in UAN (0.50 mg NO-N kg h) plots in 2009. The abundance of AO and NP decreased in 2013. There was no treatment effect on the composition of AO. Correlation analysis suggested that AOB were functionally more important than AOA, indicating the need to target AOB for efficient management of N in PL-receiving soils. Overall, the difference in nitrification between PL and UAN was mainly caused by the change in AO abundance rather than composition, and AO were not negatively affected by an increase in PL-derived trace metal concentrations.

Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria

Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4-42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (T_opt) for AOA- and AOB-supported NPs were significantly different (P<0.001), with AOA having T_opt>12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔC_P^‡) was correlated with T_opt across the eight soils, and the ΔC_P^‡ of AOB activity was significantly more negative than that of AOA activity (P<0.01). Model results predicted, and confirmatory experiments showed, a significantly lower minimum temperature (T_min) and different, albeit very similar, maximum temperature (T_max) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different T_min, but no evidence of multiple T_min values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH₃ oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments.

Effects of dicyandiamide and acetylene on N2O emissions and ammonia oxidizers in a fluvo-aquic soil applied with urea

Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are crucial for N₂O emission as they carry out the key step of nitrification. Dicyandiamide (DCD) and acetylene (C₂H₂) are typical nitrification inhibitors (NIs), while the comparative effects of these NIs on N₂O production and ammonia oxidizers' (AOB and AOA) growth are unclear. Four treatments including a control, urea, urea + DCD, and urea + C₂H₂ were set up to investigate their effect of inhibiting soil nitrification, nitrification-related N₂O emission as well as the growth of ammonia oxidizers with a fluvo-aquic soil using microcosms for 28 days. N₂O emission and net nitrification rate increased after the application of urea, but were significantly restrained in urea + NI treatments, while C₂H₂ was more effective in reducing N₂O emission and nitrification rate than DCD. The abundance of AOB, which was significantly correlated with N₂O emission and net nitrification rate, was more inhibited by C₂H₂ than DCD. Furthermore, the application of urea in all the soils had little impact on the AOA community, while obvious shifts of AOB community structure were found compared with the control. All AOB sequences fell within Nitrosospira cluster 3, and the AOA community was clustered to group 1.1b. Collectively, it indicated that application of urea combined with NIs (DCD or C₂H₂) could potentially alter N₂O emission, mainly through regulating the growth of AOB but not AOA in this fluvo-aquic soil.

Nitrification Is a Primary Driver of Nitrous Oxide Production in Laboratory Microcosms from Different Land-Use Soils

Most studies on soil N2O emissions have focused either on the quantifying of agricultural N2O fluxes or on the effect of environmental factors on N2O emissions. However, very limited information is available on how land-use will affect N2O production, and nitrifiers involved in N2O emissions in agricultural soil ecosystems. Therefore, this study aimed at evaluating the relative importance of nitrification and denitrification to N2O emissions from different land-use soils and identifying the potential underlying microbial mechanisms. A (15)N-tracing experiment was conducted under controlled laboratory conditions on four agricultural soils collected from different land-use. We measured N2O fluxes, nitrate ([Formula: see text]), and ammonium ([Formula: see text]) concentration and (15)N2O, (15)[Formula: see text], and (15)[Formula: see text] enrichment during the incubation. Quantitative PCR was used to quantify ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results showed that nitrification was the main contributor to N2O production in soils from sugarcane, dairy pasture and cereal cropping systems, while denitrification played a major role in N2O production in the vegetable soil under the experimental conditions. Nitrification contributed to 96.7% of the N2O emissions in sugarcane soil followed by 71.3% in the cereal cropping soil and 70.9% in the dairy pasture soil, while only around 20.0% of N2O was produced from nitrification in vegetable soil. The proportion of nitrified nitrogen as N2O (PN2O-value) varied across different soils, with the highest PN2O-value (0.26‰) found in the cereal cropping soil, which was around 10 times higher than that in other three systems. AOA were the abundant ammonia oxidizers, and were significantly correlated to N2O emitted from nitrification in the sugarcane soil, while AOB were significantly correlated with N2O emitted from nitrification in the cereal cropping soil. Our findings suggested that soil type and land-use might have strongly affected the relative contribution of nitrification and denitrification to N2O production from agricultural soils.

Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate on Nitrification and Nitrifiers in Two Contrasting Agricultural Soils

The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is a powerful tool that can be used to promote nitrogen (N) use efficiency and reduce N losses from agricultural systems by slowing nitrification. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrification and N2O production; however, their responses to DMPP amendment and the microbial mechanisms underlying the variable efficiencies of DMPP across different soils remain largely unknown. Here we compared the impacts of DMPP on nitrification and the dynamics of ammonia oxidizers between an acidic pasture soil and an alkaline vegetable soil using a (15)N tracing and (13)CO2-DNA-stable-isotope probing (SIP) technique. The results showed that DMPP significantly inhibited nitrification and N2O production in the vegetable soil only, and the transient inhibition was coupled with a significant decrease in AOB abundance. No significant effects on the community structure of ammonia oxidizers or the abundances of total bacteria and denitrifiers were observed in either soil. The (15)N tracing experiment revealed that autotrophic nitrification was the predominant form of nitrification in both soils. The (13)CO2-DNA-SIP results indicated the involvement of AOB in active nitrification in both soils, but DMPP inhibited the assimilation of (13)CO2 into AOB only in the vegetable soil. Our findings provide evidence that DMPP could effectively inhibit nitrification through impeding the abundance and metabolic activity of AOB in the alkaline vegetable soil but not in the acidic pasture soil, possibly due to the low AOB abundance or the adsorption of DMPP by organic matter.

IMPORTANCE

The combination of the (15)N tracing model and (13)CO2-DNA-SIP technique provides important evidence that the nitrification inhibitor DMPP could effectively inhibit nitrification and nitrous oxide emission in an alkaline soil through influencing the abundance and metabolic activity of AOB. In contrast, DMPP amendment has no significant effect on nitrification or nitrifiers in an acidic soil, potentially owing to the low abundance of AOB and the possible adsorption of DMPP by organic matter. Our findings have direct implications for improved agricultural practices through utilizing the nitrification inhibitor DMPP in appropriate situations, and they emphasize the importance of microbial communities to the efficacy of DMPP.

Effects of 30 Years of Crop Rotation and Tillage on Bacterial and Archaeal Ammonia Oxidizers

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) both mediate soil nitrification and may have specialized niches in the soil. Little is understood of how these microorganisms are affected by long-term crop rotation and tillage practices. In this study, we assessed abundance and gene expression of AOB and AOA under two contrasting crop rotations and tillage regimes at a 30-yr-old long-term experiment on a Canadian silt loam soil. Continuous corn ( L.) (CC) was compared with a corn-corn-soybean [ (L.) Merr.]-winter wheat ( L.) rotation under-seeded with red clover ( L.) (RC), with conventional tillage (CT) and no-till (NT) as subplot treatments. Soil sampling was performed during the first corn year at four time points throughout the 2010 season and at three discrete depths (0-5, 5-15, and 15-30 cm). Overall, AOA abundance was found to be more than 10 times that of AOB, although AOA transcriptional activity was below detectable levels across all treatments. Crop rotation had a marginally significant effect on AOB abundance, with 1.3 times as many gene copies under the simpler CC rotation than under the more diverse RC rotation. More pronounced effects of depth on AOB abundance and gene expression were observed under NT versus CT management, and NT supported higher abundances of total archaea and AOA than CT across the growing season. We suggest that AOB may be more functionally important than AOA in this high-input agricultural soil but that NT management can promote enhanced soil archaeal populations.

Nitric oxide scavengers differentially inhibit ammonia oxidation in ammonia-oxidizing archaea and bacteria

Differential inhibitors are important for measuring the relative contributions of microbial groups, such as ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), to biogeochemical processes in environmental samples. In particular, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO) represents a nitric oxide scavenger used for the specific inhibition of AOA, implicating nitric oxide as an intermediate of thaumarchaeotal ammonia oxidation. This study investigated four alternative nitric oxide scavengers for their ability to differentially inhibit AOA and AOB in comparison to PTIO. Caffeic acid, curcumin, methylene blue hydrate and trolox were tested onNitrosopumilus maritimus, two unpublished AOA representatives (AOA-6f and AOA-G6) as well as the AOB representative Nitrosomonas europaea All four scavengers inhibited ammonia oxidation by AOA at lower concentrations than for AOB. In particular, differential inhibition of AOA and AOB by caffeic acid (100 μM) and methylene blue hydrate (3 μM) was comparable to carboxy-PTIO (100 μM) in pure and enrichment culture incubations. However, when added to aquarium sponge biofilm microcosms, both scavengers were unable to inhibit ammonia oxidation consistently, likely due to degradation of the inhibitors themselves. This study provides evidence that a variety of nitric oxide scavengers result in differential inhibition of ammonia oxidation in AOA and AOB, and provides support to the proposed role of nitric oxide as a key intermediate in the thaumarchaeotal ammonia oxidation pathway.